Layering? Just go to Data => Layers, set the screen you want to use (upper number is "map", bottom number is the screen). Then the bottom bar's Layer section gets a new layer tickable. Tick it, and now everything you place on the screen will be placed on the layer. Why is it good?
1. Transparent colour gets 100% transparent
2. Ticking the "transparent" box makes the whole layer see-through
3. You can place multiple things on the same place
4. You can place things above Link's head, even above flying enemies (Layers 1 and 2 are below Link and push flagged combos, but above Layer 0. Layers 3 and 4 are above Link's head but below "overhead" combos and flying enemies. Layers 5 and 6 are absolute.)
I really don't think you could make a big quest without these features...
As for tilesets... err, were you using Classic for these character sprites?
If you want to learn tilesets, oh well... Play Hero of Dreams for Pure-PTUX knowledge, play Shadows of Dawn for PTUX+ knowledge, play Ballad of a Bloodline for DoR++ knowledge, play Lost Isle for PTUX++ knowledge, play Shadow Knights for GB knowledge.