shoot, I just wrote like a whole tutorial for you about tileset settings, but I lost it. Oh well, let's try again.
Think of it this way: there are three levels: stuff you step on, stuff you bump into, and stuff you walk under. When you go to the database (F8), click Tileset (Chipset for 2k) and select the chipset you are having problems with. Click Passibility, and now you can click on a tile to change it's level. When it is a circle, you walk over it. When it is an X, you can't walk through it. When it is a star, you walk under it. Make sure all your floor tiles are circles. Did that help?
Also, I am writing a tutorial on the basics and advanced aspects of pokemon game making. It won't be ready for a long time though.