For schools that offer the joint MD/MPH program, you don't need to fill out the SOPHAS. Usually they either just have you indicate you're interested in the dual degree program, or complete an additional essay on why you want an MPH, or something along that line. Other schools that offer the joint degree have you apply directly to the dept granting the MPH (usually done in January). Your best bet is to look at the website of each school you're applying to that offers such programs.
Now, if you're also applying to schools that don't offer a joint degree, it's not uncommon for students to take a leave of absence after M2 to pursue the MPH at another institution and then return to finish the program. Unfortunately, I think that for this option, it usually takes 2yrs (instead of 1yr in a joint-degree prgm) to complete the MPH (not an expert here, so someone else can chime in).