That would work, but might not give you the port area you were hoping for at 25 sq.in.
Personally, I think it would be a better idea to use a single 6" port, and tune to approximately 34hz (You won't hear much of a difference).
Unfortunately, both of those ports will take up a decent amount of space. Both will take up about .4 cu.ft. of airspace. If your box is 2.5 cubic feet, you are left with 2.1 after port displacement. Lets say another .15 for driver displacement and you are now at 1.95 cu.ft. That will give you a final tuning of about 37hz. That is still a decent tuning, but will be noticeably more peaky than one at 32 like you were hoping for.
At this point, your options are to either:
1. Live with less port area in order to get it to your desired tuning, and try to minimize port noise by keeping the port as far away as possible.
2. Replace your 12" Q with a 10" driver so that you can better use the airspace you have.
3. Use a different subwoofer.
If you want to keep the 12" Q, the box that you have, AND maintain a 32hz tuning, your only choice would be to use less port area. Probably about 20-25 sq.in. total. Although I haven't used a Fi Q before, I think your subwoofer will still be plenty listenable with that port area. See if you can find some users with a box similar to yours, and see what they have to say about port noise.