The overwhelming majority of allopathic PM&R programs accept COMLEX licensing exams in lieu of the USMLEs, and generally speaking, PM&R is considered very "D.O. friendly". That being said, some programs may require USMLE Step 1, and it would be a good idea to do your leg work and read up/call programs to find out what their requirements are before you apply there.
In terms of your internship year, as a D.O. you currently have two options -- go through the AOA Match and apply for an osteopathic internship, or go through the ACGME match for your intern year. You must be aware though, that if you match an osteopathic internship through the AOA match, you will not be eligible to match an internship year through the ACGME match, nor will you be able to match into allopathic categorical (programs that are 4 years in length because they include the internship) PM&R programs. This is because the AOA match rules stipulate that you cannot match into an AOA program and ACGME program that
start at the same time (i.e. can't match an osteo trad rotating internship and ACGME categorical PM&R program).
What osteopathic candidates will do is either:
A) give up on the AOA match and go straight for the ACGME match and rank the 4 year and 3 year ACGME PM&R programs at the same time, hope they match a 4 year one so their internship is included. If they match a 3 year PM&R program and need an internship, they then SOAP/scramble into whats left of the ACGME internships or the AOA Osteo Trad Rotating years.
-- The overwhelming majority of DO grads that I know who applied into PM&R and did this ended up matching 3 year advanced ACGME PM&R programs, and scrambled into AOA Internships. Frankly, there are less of the categorical (4 year) PM&R program spots compared to the advanced (3 year) PM&R spots, and as such, these categorical spots are much more competitive to get.
B) enter the AOA match, match into an osteopathic TRI year so their internship is set, and then rank only the 3 year (advanced) ACGME PM&R programs. Again, if you match an AOA Internship you will not be eligible to match into allopathic internships or 4 year (categorical) PM&R programs because of what I mentioned above.
To answer your other question, when it comes time to ranking ACGME advanced and categorical programs, you will rank them at the same time.
When you rank the advanced programs, you have the option of submitting a separate rank list for internships (called a "supplemental rank order list"), that gets used IF and ONLY IF you match an advanced program.
Furthermore, the system allows you to have different supplemental rank order lists, so that if you desire, no two advanced programs have to have the same internship rank order list.
Thus, you can have different internship program rank lists for each advanced program. I.E. Your advanced program in Texas has a certain internship ROL, and your advanced program in NY has a different ROL, if you want to try to include geography or hospital preferences into the match equation.
For osteopathic candidates, there are certain things to consider regarding internships. Some states require an osteopathic internship in order to practice there, though the AOA has a process in place for helping you get your allopathic internship approved in lieu of an osteopathic one, if you are to choose that route.
Another thing for osteopathic grads and foreign medical grads to consider, is that the rules regarding entry into allopathic residency programs may change, and you may be required to do an allopathic internship prior to entry into an allopathic residency program. This is still up for debate by the ACGME and last I checked, a final vote/decision on the issue has not been sorted out.
The AAPMR has an EXCELLENT website on how to apply for PM&R Residency, including specific information on intern year requirements, options for allopathic and osteopathic students, and special osteopathic considerations.
http://www.aapmr.org/career/students/career-planning/Pages/guide-to-apply.aspx