Maybe if you tell us what all these images are for we may be able to help a bit better I think. I'm guessing it's a tiled engine? That may account for the "1200 16x16 images" in which case I must ask what your game's screen resolution with 16x16 sized sprites. So what are the 1200 alpha blended images?

It almost seems like you are trying to swallow a whale without knowing how to... well... "fish" *ahem* pardon the expression. So lets start with what type of game it is and what gameplay features are you trying to put into it?