I'm not too clear on what you're trying to do exactly when you say take out the background (I think I do but there's a reason the backgrounds are colored, unless your character is gonna be 32bit and not using transparency)
There's a couple of ways to do that and different reasons for the different ways, hence why I'm saying how to like go about that. If it's gonna be indexed
Anyway, Photoshop and FF3 can do the same stuff, for the most part. If you're just gonna cut the fx then you may be better off using FF3. It doesn't sound like you're too experienced with either so I'd recommend just keeping things simple and use that.
And hey, don't be afraid to make mistakes. That's how you learn ?