I am "Mystic Rhodan Winterblossom the Red, Romantic Gazer", or just Rhodan. I'm a wizard of the Red Hedge variety.
Skills are arranged in a tree. Before you can raise a skill individually, you have to have reached a certain level in the main branch.
So to level up fighting.melee.swords, you have to have fighting at least lvl 5 and melee at least level 10 to put xp in swords. Levelling a branch also levels the inner skills, though, you just can't specify right away.
This is not the case for crafts, people and adventuring skills. They can be levelled a bit more individually without having to level the outer branch.
Skills can be learned in four ways:
At your Guild:
Here you can learn skills relevant to your Guild up to level 50 for some xp and a small fee.
You can learn skills specific to your Specialisation (Mugger, Samurai, Ninja, Wizards of the Last Order,...) up to level 300.
Most other skills can be learned to level 10 or 5 as well.
From others:
"learn x.x.x from player" allows you to learn from other players. The amount you can learn from them is the average between their bonus in the skill and their teaching skills. For someone with no skill in teaching, you can learn up to half their bonus.
From yourself:
"teach me x.x.x" (or something) Most expensive xp-wise, but still useful at times, especially to give yourself a little boost at lower levels.
From TMs:
A TM is a free skill increase when you use a skill at a level where you are equally likely to succeed as to fail, training the skill as it were. Skills like crafting train well this way.
Commands can be learned in two ways:
At your Guild:
Once you join or reach a specific Guild level or skill level, certain NPCs will teach you specific commands. Usually you can just ask them about it.
From other players:
Commands from other guilds (except the unique ones) have to be learned from other players. If you have the right skills and they have enough skills, they can teach you. Usually it's enough to walk into the Mended Drum when it's a bit busier and just ask the general public.
For fixing scavenged stuff, it's best to stick to clothes, as they can be fixed for free and for no skill at the Temple of Gapp. Go inside and put your clothes on the altar, and Gapp will mend them for you. It might cost some gp, but you can just wait a bit for it to recharge.
Fixing weapons/other junk usually has no worthwhile profit margin and most stuff of value will be clothes anyways.