1.Against certain characters, what are some of the area's of the stage I want to control? Where should I be trying to push my opponent?
Generally you should be trying to push everyone towards the edge. No character had an advantage over puff there and you can gimp basically everyone.
Your goal should be to force opponents offstage so you can exploit your advantages there. The ledge should be your natural habitat.
More specific knowledge:
Against
spacies you need to control the area diagonally above them (stuff their jumps OOS and otherwise) and platforms. Without those 2 things spacies are left with substantially limited options. Try not to cross them up or stay directly above them for very long, they can convert those situations into punishes against you. Also, dont land with an aerial out vs Fox. You WILL get grabbed.
Against
Marth you want to stay in the area just outside sword range and bait laggy attacks with spacing and feints. Wavedash OOS is your bread and butter in this matchup. You can also duck jump cancelled grabs and trade gimp his recovery pretty easily. Marth is very fragile off stage and can't do much to puff out there, so chase him and follow up when he's trying to recover.
Against
Sheik, stay out of the downward angle from her airborne approach. Needles convert to possibly the only safe grabs vs puff.
Take the ledge when sheik is recovering. She has a laggy recovery when she lands on stage that is really punishable.
Try to recover high so sheik can't hit you with drop> jump> bair.
Duck a lot, a missed JC grab is a free rest.
Weave Nairs in frequently too, they are very safe in this match.
Against
Falcon, stay out of the area diagonally above him, it is uair/knee range and incredibly dangerous. Try to stuff his jumps before he gets Nairs or dairs out. You want to stay low, but airborne. Duck grabs whenever possible and try very hard to not get grabbed at all, a good falcon is guaranteed a knee after a dthrow if he reacts to your DI correctly.
Don't land with an aerial out, dashdancing falcons can exploit your landing lag and grab.
Take the ledge when he's offstage and try to gimp if at all possible. Falcon's recovery isn't as fragile as Marth's, but it is definitely exploitable too (long landing lag, predictable path).
2.After taking a stock, where do I want to place myself on the stage? What do I need to focus on when coming back on stage?
If you want to be safe take the ledge after taking a stock. It starts the stock with you in a very safe defensive position and nobody wants to mess with a puff on a ledge, even during invincibility.
When recovering, recover high, as a general rule. You can maintain altitude easily with pound and nobody will be able to intercept. Landing is another story, but don't be afraid to mix in an airdodge or aerial to land safely.
3.What are the best ways to utilize my airspeed when playing a retreating/chasing game against my opponent?
Stay airborne as much as possible, filling most of your jumps with attacks or threats of attacks. Weave in and out of your opponents range, baiting attacks or stuffing them before they happen. Land with autocancelled nair, waveland, or ledge cancel onto more jumps. Stay mobile and dont commit to a risky attack.
There is more stuff to learn, for sure. A lot of it comes from experience though. Good luck.