If you don't have a huge amount of skill creating resources (and not just visual resources, but scripts and music as well) the best thing you can do is plan ahead. Grab a notebook/open a word processor and write down everything you want to accomplish with your game, focusing heavily on a progression route i.e. all the towns, dungeons, and other locations the player is going to visit. Then evaluate the resources available to you, figuring out how they'll fit with those locations and if you'll need to make changes, whether to the resources or to the locations themselves. It'll save you trouble down the road.
Always keep in mind that part of developing a game is learning to work within your means, and sometimes you have to make sacrifices. You might have to strike a dungeon idea down because you don't have the proper tiles to pull it off. Cut your losses and find a way to adapt.
Of course, it also helps to choose a style that you know you can easily edit if it comes down to it. Personally, I'm horrible at editing the "painterly" style, so I only use pixel art resources because I know I can edit them. I've learned to take resources from various sources--the XP RTP, the DS RTP, resource blogs--and edit them so they blend together. Take what you can get and be thrifty with it!
