I have Rock Boots and Scuba Pro Jet fins as well. I can use my boots with my fins because I bought the fins large enough (just so) to do so and also use them with booties. I find the Boots to be somewhat uncomfortable and another bulky thing I have to carry and put on.
I have not yet tried out this combo, but I bought some oversized SCUBA "socks" to put over the foot of my DUI drysuit which I think will be more comfortable than the Boots and still allow me to comfortably use my current fins. Frankly, unless I’m shore diving and need to do somewalking over sharp rocks to get in the water, I don’t really see the need for wearing a pair of boots to go diving from boat. I intend for the relatively cheap socks to be sacrificial protection for the foot of the dry suit.