I decided immediately afterwards to place a big array of cage, and upright spike traps just before the entrance to the caverns, just to be safe, and still be able to mine out the materials there.
This is the main way to secure the first cavern layer. Nothing in the first layer is a true danger to your fort. In fact, most wildlife in the first cavern layer is more interested in running from your dorfs than eating them. But GCS are scary! You say, yes they can be. However, GCS (along with trolls and crocs) are building destroyers. They have a raging hate-boner for built structures (not walls/bridges/floors, but things like statues and doors). So if you place a few (wooden) doors-to-nowhere around the edge of the caverns and then put a few cage traps around them, they'll act as magnets to snare these dangerous critters. It helps to dig a few tiles into the rock near the map edge (where they spawn from). So when that big bad croc enters the map, the first thing he sees is some BASTARD wooden door taunting him and not a tasty dorf to snack on. He charges that ASSHOLE door and falls right into your trap.
Those reptile-men were never an actual danger to your fort either. They never actually move around. You could have just ignored them and they'd have returned the favor. At most you could have walled them in to keep your dorfs from wandering too close to them.
Now for the GCS- its probably best you don't tame it for now. You'll need two to breed (they can breed now), but taming one makes it a little harder to farm silk from. The gist of silk farming is to put a GCS in a locked room lined with fortifications on one side. You'll also build a small retracting bridge directly on the opposite side of the fortifications to block line-of-sight as needed. Then you place a target that is hostile to the GCS on the other side of the bridge. Now, if the GCS is tamed, this needs to be a critter hostile to your fort (wild animal/gobbo/etc). If the GCS is wild itself, you can just chain a puppy up nearby. Now, with the bridge up (blocking line of sight) put the bait in place. With all of your dorfs safely out of the room, lower the bridge and let the GCS blast away. It'll sit there and spew silky gold for... well until it dies in a couple years. Any time you want to collect the silk, just raise the bridge and send in some weavers. You shouldn't need to recapture the GCS unless you find another to tame it. To recapture, you can probably just use a raised bridge blocking a wooden building with traps in front of it like you did in the caverns.
Now, for that giant toad. You have three options. You can let your military get some live training killing it (they aren't too dangerous). You can tame it and then "pasture" it near the front of your fort as a fodder. The easiest option is to tame it once (semi-wild is fine), then lead it to your butchers shop. The very worst of training will still last long enough to safely butcher the animal, but putting the animal training zone near your butchers can't hurt- at all. Please do this! >.> Back on point, all cave critters have value multipliers on their parts- I think toads are x4? So crafts, armor, and food made from butchered toad parts are going to fetch a fair price. This is what I do with most of my tameable cave crittes I get from traps. You can feed an entire fortress on cavern meat with enough traps... I've also done very well for myself on metal-less embarks using a menagerie of semi-trained cavern critters as fodder. I've even defeated a couple of early sieges just with cave crocs, elk birds, draaltha, and giant toads. It helps to build a partial wall to block line-of-sight from archers, thus forcing them into melee range before they can open fire. The best use of the cave critters is to station your marksdorfs behind them. While the crocs are keeping the goblin lashers busy, your marksdorfs can do their work.
Hmmm I -suppose- you could also make pets out of the critters. Only a few of the cavern critters are hunting/war trainable (jabberer, giant cave swallow/bat), but the others can serve as good distractions to let their owner get away. Just overlap an animal training zone with your meeting hall and pasture the (mostly) trained animals there that you want adopted.
Almost forgot- as has been mentioned you can cage-trap FB's with GCS. In this case it probably is best to tame the GCS for easier replacement. Its similar to the silk farm, except you want the GCS to be shooting at a target adjacent to some set cage traps. You want the webbing to land right on top of the traps. Then, the big-bad FB comes stomping into your fort, gets caught in the webbing, then immediately gets snared by the trap. Stunned/webbed entities lose their "trapavoid" tag. You can get similar results from controlled cave-ins and collapsing floors. CAUTION! Creatuers that have no-stun (all FB/Titans) can't be trapped this way. Creatures that use webs themselves (GCS+any web spewing FB/titan) will also have "Webimmune" that prevents them from being trapped this way as well. So don't think your webbed cage-trap line makes you invulnerable, because a web-spewwing FB will saunter right through them. Otherwise, it works like a charm letting you capture insanely deadly FB's (like that flying steel-skinned poison spewer...) without much hassle. Now, you don't want farking CRUNDLES falling into your webbed traps, so I'd keep the web-trap line sealed off. Then, when you see an FB spawn, double check that it isn't webimmune (if it can spew webs, its immune) then seal your main trap corridor and open the webbed one.