1) How long do I have to "charge" or "hold -down- for" to pull of the move?
Charge time is about 1 second (real time, not based on the timer for the round). If you've played charge characters in Street Fighter games, the charge time in KOF is about half of that. If you've played charge characters in Arcana Heart games, the charge time is about the same.
2) And also, what would you mean by juggle state? Would that mean that they are still attackable before the collapse or something along the lines of that?
Yep, though there is a little caveat.
There are (I think) two types of juggles in XIII, normal juggles and anywhere juggles. Normal juggles work exactly like you said (a move puts your opponent in juggle state, and then you can hit them with whatever before they hit the ground). Anywhere juggles are certain special moves (like Vice's EX Decide or Elizabeth's Grand Rafale DM) that will always hit an airborne opponent, even if they aren't in a juggle state. For instance, any move can juggle after a counterhit j.CD, but only anywhere juggles will connect after a non-counterhit j.CD.
Moves with anywhere juggle properties should all be noted in the wiki.
I guess my main problem now is getting used to the joystick! 
Although at times I seem to be failing to get my specials right, I think I'm starting to get the hang of it~
If you haven't used an arcade stick much before, it can definitely take time to get used to it. You might want to look into getting a cheap one just to practice with using it at home (where you might be able to use games with input display in practice mode and where you'll at least not be playing money just to get used to a stick *laughs* ). If you really want to use a stick for console play as well, though, I'd advise spending a little more (if necessary) to get a good one, since upgrading cheap parts to good quality ones will end up costing a similar amount anyway.
Looking at the technical reference I'm assuming that those aren't all the possible cancels?
Off the top of my head, I think the technical reference videos show all of the moves that can be drive/super/max canceled, but not all of the possible cancel timings. I'm not sure how many characters are affected by that off the top of my head (characters who mostly use single-hit moves like Shen or Leona don't care, but it can make a difference for someone like Mature, who gets different effects depending on when she cancels the last part of qcb+Px3), but I'm sure asking in the character threads for whoever you want to use will get you the answer to that.
Once again thanks for the replies and I'll take that into heart when I practice further! Of course if you have any more tips please do help me out! xD
This isn't the first thing you need to do (just get comfortable with doing regular inputs and cancels for now), but I'd definitely recommend taking some time eventually to try finding out how much time you can put between the stick input and pushing the button(s) to make a special come out. This is useful for hitconfirming (reacting to a move hitting and going into a combo), since you can autopilot a string like (with Shen) s.C, f+B, hcb~f, and then only press the A/C button if you saw the first part hitting.
