Thanks everyone..........Looks like I will be joining another forum
With all due respect, this is an ignorant statement. Please allow people time to post. A) You only allowed ~3 hours for someone to post. B) The time frame during which you posted is not the "prime time" for this forum, per se. Everyone here is kind, patient, and more than willing to help--you just have to be understanding enough to give them a chance. I'll ask that you please keep all of this in mind and change your attitude toward posters here.
Now for your question. If you plan on having a refugium, you'll want to place it in the first, larger compartment. That will limit other options, however, such as a protein skimmer, which will need the space that the refugium would occupy. However, the refugium would probably do your tank a bit more immediate good than the skimmer, the latter of which only indirectly reduces nitrate and phosphate (and takes much longer to have an effect).