I'm not exactly sure what the problem is, but have you tried switching between these three buttons on the toolbar? (See attachment)
The green one is for things that will go underneath -e.g floors, walls, etc, the blue one is for things that will sit on top of that -books, tables, phones... and the third is for events. If you want to place something on top of an item you've placed down in the blue, upper tile layer, create an events, set its graphic to what you want, and click ok. Then that will appear over the tile in the upper tile layer.
Does that help?
If you search on google under RPG Maker you can find heaps of tutorials which might help you out. I learned heaps of stuff about how to use switches, variables etc. You can also find a lot of custom-made graphics. A character generator? Here's the address of a site with one:
http://charas-project.net/ You'll find the character generators just under the banner heading and above the google ads (no pictures, just articles). I don't remember liking it that much, but see what you think. Generally I just find a model I like and change the hair/clothes/eyes using paint.
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