Welcome from Northern Michigan!
Kudos to you for jumping in and designing your own squares! I draw all my quilts on graph paper with colored pencils. Then I assign each square a value- usually 3 inches- and then add my seam allowance. I don't make each square on it's own piece of paper unless I am trying to draw my own applique design.
I attached one so you can see how I do it.
As far as each square having it's own color scheme, I think you will be fine- IMO your color choices are what make your quilt "yours". I do think that setting them on white or a solid color might help with letting the eye have some resting spots, but that is just me. If you go to Flickr and search for Sampler Quilts I bet you would get a lot of inspiration.
http://www.flickr.com/photos/30239158@N05/2886035802/
For instance in this quilt they used a lot of different colors, but the black setting makes it look nice and tidy. (To me anyway. Tidy is a pretty subjective term- LOL!)
Welcome and you will have to show us pictures of your quilt when it's done, or even as you are working on it! We love pictures!