How to set threshold in ImageJ for quantifying relative fluorescence?
You need to normalize both images to the background. This can be done in many softwares including photoshop.

When I was learning this starting to do it with something more simple like SDS page protein bands helped me a lot. The principles are the same you are still subtracting background. Look at this tutorial:

http://m.youtube.com/watch?v=JlR5v-DsTds

However, when analyzing intensity values in fluorescent microscopy the most important parameter is area of your analysis. This needs to be an objectively applied as much as possible, and that can be by increasing the number of replicates whose area you analyze. Your going to look at pixel intensities for many many cells and average those intensities. Using the imagej cell counter plug-in is helpful to see how to determine cell area.