Managing the military equipment can be a tricky business. Having gotten fully used to it now I feel confident that when I set it up it will happen the way I want it to. The last 3 forts ive started recently have had 0 issues but probably the 10 before it I was still learning.
1) The pickup equipment is a task a dwarf assigns itself and completes(hopefully) when they actually go and pickup equipment. I have seen more than one mention of dwarves dropping their equipment when set to inactive (possible bug) but I have never seen this myself. It can also take a very long time for a dwarf to complete "pickup equipment" depending (presumably) upon the equipment that the dwarf is set to use.
My best guess for why your dwarves are not fully utilising the metal armour youve assigned to them is that you dont have the option "replace clothing" set. On the equipment screen there is a setting at the top entitled "replace clothing" activated with the "r" key. This will likely solve your issues with dwarves assigned metal armour wearing silk. The reason for this is that rmour is rather complicated, with up to 3 "layers" per slot and some equipment preventing the wearing of another. The wiki page describes the layers and combinations. Im not totally au fait with it but I know how to work around it. Also clothing counts as an armour layer, and clothing must be worn to prevent very unhappy dwarves, so when you first equip armour there is often a clash which is usually fixed by the replace clothing option.
2) The issue of dwarves not picking up your "discarded" weapons and armour could be due to the orders ( "o" key). You can tell dwarves to ignore stuff outside the fort, as well as various other options. Again im not fully au fait with everything there I just sort of know how to work around it. If the stuff is "claimed", there is a path to it and you have a stockpile dwarves should be grabbing it. Orders would be my best geuss why they are not. Have a play with that screen and try and make sense of it.
3) I use danger rooms, it took me a few forts to get these right. They are described reasonably well on the wiki, I use it to get mine set up. basically what you want it a 1x4 tunnel, an armour stand or weapon rack at the end, a door blocking it off, a 1 tile gap followed by another door. You lock the door next to the weapon rack. If you then make the door internal ( "q" over the door youll see) and create a barracks, the barracks area extends past the locked door (if its set to internal) to the "gap". Then you set up a trap, "b" key then "T" for traps and then select upright spear (I think i forget which option but again youll see in the menu). You want to make sure you have made "wooden training spears" at your carpenters workshop. Put 10 in the trap. Dont use upright spikes as theyll do too much damage. Once you have your trap and barracks link a lever to the upright spear trap.
Now arrange for your squad to train at the barracks, once all dwarves have equipped and filed into the "gap", lock the outside door so children pets and so on dont accidentally walk into the danger room area whilst training is in progress. Then set the linked lever to be pulled and repeat the job (hit r on the job list).
Now what you should see is massive gains in shield user (if shields equipped) very quickly. Some people consider it an exploit. I love X Men and I feel that theres nothing wrong with the concept of a danger room but probably the gains are too quick.
4) Marksdwarves are a different kettle of fish. I dont tend to have problems with them but some people report difficulties. The direction of fire is important with archery ranges. Make sure this is set to a direction that makes sense, ie if your archery rangers are against a wall running in a line east to west, they should be firing from the south to the north, not vice versa and not east to west either.
They require bolts being assigned to them as well as crossbows, and the bolts can be assigned to (T)raining and (C)ombat seperately. I usually have all my civillians equipped with crossbows and leave their squads on inactive. they train occasionally around other jobs they do. I think if you wanted mroe rapid gains you would need to set them to active.
C being lit up means they will use that ammunition for combat, T for training. To shoot, they will need C lit up. Be aware that a marksdwarf that runs out of ammo will attempt to charge and melee with his crossbow. I keep marks dwarves on the walls of my fort behind fortifications. This usually prevents them from engaging in close combat when they run out of ammo.
5) Im not 100 percent certain but I dont think you can set up patrol routes within the vanilla game. DF Hack adds such functionality I believe. Thats a whole nother book of learning to assimilate. Id say dont worry too much about patrols for now, I dont do it at all in my forts,
yet.
6) Like the marksdwarves, I think dwarves basically wont retreat once engaged. Id suggest to keep males only in melee squads, to prevent undesireable infant mortality during engagements. I keep all my forts dwarven ladies in Xbow squads and mostly keep them out of melee, as mentioned supporting my melee squads with missile support from the walls.
7) No formations as yet, im looking forward to the day when we will get formations. im not aware of any DF hackery that "does" formations.
armour and weapons dont currently receive damage like clothing (damaged clothing has x, X, xx or XX surrounding its name). If you have any weapons or armour that have x's its likely because theyve been stored in a refuse pile someway somehow. All items will slowly rot away in a refuse pile. Damaged clothing is trash, it can be sold to caravans, atomsmashed or dumped in lava. new clothing is the order of the day. Armour and weapons have an infinitely long useful life (currently).
9) The fact that youve found silver gold and platinum could be all the metals that are on your site. I dont think there is a set Z level for deep metals, the available Z levels vary depending on the site.
DF Hack has a prospect all option that tells you pretty accurately whats on an embark site from the embark screen (before youve actually begun building a fort), also will tell you once you have embarked and started building. Also has an option to "reveal" all squares, so you can easily see what and where the metal is contained in your site.
10) Siege engines are currently a waste of time, dont bother with them.
DF Hack is a command line (text based) companion program to DF. you have to alt tab to it during game to use its functions. if you get the right lazy newb pack itll have df hack built in. Im by no means an expert or qualified to help beyond what ive suggested. I found it very daunting at first but by playing with it I got used to it and learned how to use it to ridiculously good effect to the point where I now wouldnt want to play without it. google df hack, browse to the github link and youll find a list of available DF Hack commands. I think this is usually contained within a DF hack containing LNP.
Remember, dwarf fortress is free, currently under active development and has been so for plenty of years so far and Toady plans to continue in this vein for possibly up to another 20 years or until hes satisfied with the game as finished, whichever comes first, donations pending.
So there are bugs, incomplete features and some design aspects that are crying out for an overhaul. DF hack helps to work around some of the bugs and design flaws but no other game can touch dwarf fortress. ie DF hack and Dwarf fortress are worth the trouble. But you probably know that already...
hope that helps and good luck.