Oh you're on Chapter 2 now? *ahem* I'll give you some tips. (I'll try not to spoil anything, sorry if I do)
As for upgrading:
Goombella gets Multibonk, a move which is essentially her version of Power Bounce. Costs 3 FP If you are good at timing jumps, then I'd recommend upgrading her. *On bosses, Power Bounce/Multibonk are limited to a certain amount of jumps in a row. Goombella's HP will go from 10 to 20. Her Headbonk now does 2 damage each and Multibonk will start at 2 damage then decrease to 1 damage each bounce after that. (This move cannot hurt Spiky enemies :p)
Koops get Shell Shield, a move which will protect Mario from attacks. Costs 4 FP. The shell takes damage for Mario instead. Unfortunately Mario cannot guard/super guard to reduce the damage the shell takes and it's hard to time it to the center, so I don't find it too useful. Koops' HP goes from 10 to 15. His Shell Toss and Power Shell now do 3 damage.
Flurrie gets Lip Lock, a move which drains the enemy's HP and adds it to her own. Costs 3 FP. The action command is kinda weird, you have to hold A when the star appears and release when the star is gone (Holding A when the star is gone will drain the meter, so be careful) and fill it up within a time limit. It does 4 damage, AND there is a bonus: It pierces enemy defense. Meaning that it will do 4 damage regardless of the enemy's defense. To a certain extent, it cannot attack spiky enemies, but only if their whole body is covered with it or if the spikes are like on the front (for example clefts) but you can attack some spiky enemies, such as spiky goombas or Piranha Plants.
*The damage dealt is assuming that they are normal (as in don't have their power raised or anything)
As for Chapter 2...
IIRC there are 5 Shine Sprites. (correct me if I'm wrong) I believe there's 1 in the Boggly Woods and 4 in the Great Tree. I'm pretty sure you've gotten the one where in Boggly Woods where you fire Koops to get it :P There's 1 in the room where the bubbles are, 1 in the room where there's a giant black thing. (use Flurrie to blow it away, then use the Paper Plane) The last two... well I'll let you figure out for yourself. =P
The boss can easily be taken down if you have lots of HP Drain items (if you haven't used it yet, save that thunder rage you found and get the HP Drains). He does have 30 HP and a defense of 1, but HP Drains do pierce his defense and they do 5 damage. However, he can summon some things (kinda like bullet bills) that can attack you for quite a bit of damage. If he summons them and you don't kill them, they will do 4 damage. And there are 2 of them. (This is why I save the Thunder Rage to attack both the missile like things and the boss) Fortunately they have little HP (IIRC 2 HP) so if you don't have that Thunder Rage, give up a turn of attacking the boss for taking out the bullets.
There is a badge in the room where the door to the shop is. You know that red block? Well, there's a hidden block underneath it. Hit it with Koops then hit the badge block. You'll get a nice badge.
Hope this helped! :D (And hopefully didn't spoil anything, if I did, I apologize)