My understanding is that you need to rank both if you are interested in both. My only question is whether the programs will rank us for both tracks (or will they "help" us decide).

Trigen is right.

Many programs who have both a 5 and 6 year track have different NMRP numbers for each.

Our program's policy is not to exclude a 6-year applicant from the 5-year track (or visa versa), especially if the applicant is well liked.

It may be worth while contacting the program director at the programs you are considering to ask. Some directors may give you a sense how the program sees you fitting in there (5-yr vs. 6-yr).

Good Luck.