Multiple transparent images that look like one image
An example image would be a flower, where the stem, leaves, and petals where all able for me to change their colors upon user input, but which other than the color changes would like like a single image in the website display.
Really would appreciate help and suggestions with this.
I doubt you'll be able to use transparency and background colors unless the regions that change color are very simple and never overlap.
I'm not a graphics guru, but I suspect that you'll need to create/extract masks for each region that will change colors and then use a server-based graphics library like GD or ImageMagick to fill the appropriate mask(s) and then composite it with a base image. I've never done it myself, but I've seen sites that have. It might take some time, but I bet if you do some serious searching that you'll be able to find a ready-made script for this process, and if you're very lucky, an online tutorial. Good luck!
Image maps might be incorporated into the design, but that doesn't address the issue of changing the color in selected regions. Similarly, I'm afraid slicing is probably inadequate unless the regions to be colored are rectangular. When I think of this topic, I'm reminded of websites I've seen from the car manufacturers who can display their cars with different body colors. While they could simply replace the images as needed, my impression is that they were doing color fills. There are other sites that display maps of the world or the US states where the colors change. In any case, it's a good way to think of the problem because these are the kind of irregularly-shaped objects that I think the OP has to work with.