First off, I have to assume that you are running a supplemental brake system that uses the CRV's battery for activation. If so, this will deplete the CRV's OEM battery fairly quickly, and you can't disconnect it if you want your braking system to work.
My overkill solution to the dead battery problem was to buy a deep cycle battery which I use to power up my Even Brake toad braking system. I back feed the deep cycle battery into the CRV electrical system. I have a battery cutoff switch on the CRV starting battery which I disconnect when the deep cycle "braking battery" is hooked up. The radio codes and clock stay powered up and the toad can be pulled along for hours without worrying that it won't start. After we hit the campground, we just crank down the battery cutoff, powering the CRV with the starting battery, unhook the deep cycle braking battery, and off we go.
I have a smart battery charger that I hook up when we're plugged in at a campsite to recharge the braking battery. I realize this is not as easy a solution as having a 12 volt feed from the RV to the toad, but this solution was our answer when we had a dead battery out on the road (in Nowhere USA) with no easy option to wire a 12 volt feed from the RV to the toad.
So, the upshot is, you have to power your toad braking system. You need a source of power that will still allow you to start your toad at the end of your trip. Some folks stop and start up the toad every 2 to 3 hours to charge up the battery and this works. But if you plan on longer jumps between rest stops or campsites you will need to find a way to power your braking system that doesn't deplete your toad's starting battery. A 12 volt feed from some source to the toad (from the RV or a 2nd battery) will allow you to disconnect the toad battery. Lacking that, you have to keep the toad battery connected. I do not recommend towing without a powered supplemental brake in your CRV! Good luck with finding what works best for you.