Several years ago, my testosterone was low while I was in an extended flare. I supplemented with gel for about
a year, went off the testoterone to see if my own levels would recover, and they did.
I went to a number of specialists at the time, and the only thing that pointed to the low testosterone was active colitis wearing just about everything down.
The gel's not bad, and if the gel patches work for you, great, but they gave me terrible chemical burns. It worked better as a stand-alone gel. I don't see why insurance won't cover it, but there are compounding pharmacies that can do it cheaper if you end up having to pay out of pocket.
I would avoid the injections since you will be on a rollercoaster of high testosterone at the beginning of the injection cycle and low testosterone at the end of it.
If you're on testosterone long term, I would see someone who specializes in testosterone. (If you think getting a GI who understands IBD is a trial, getting someone who understands low testosterone is even harder.) There are a couple of specialists in the US; John Crisler is recommended almost universally. (He's eccentric, but he _knows_ testosterone.)
Above all, you want age-appropriate supplementation. Some docs will supplement until your numbers are in the lower range of normal. If you're younger, you want the higher range of normal.