I'll answer a couple of your questions; don't know enough specifics of the Atlas system to answer the rest.
First of all - are your blocks insulated in both rails or just one?
If insulated in both, you could remove your insulated rail joiners and block wiring, but why bother if the track is working fine? By leaving it, you can isolate DCC problems to a particular block. You can also replace one powerpack with your DCC system and leave the other one to give the opportunity to run either DCC or DC for a while. I recommend doing all blocks and all locos on the layout either DC or DCC, but not a combination at any given point in time.
If you do not have both rails insulated, you can either insulate the second rail and do as I suggested in the previous paragraph, or remove all your insulated rail joiners for DCC. This leaves your layout as one large block/power district, except for the reversing loop which remains insulated in both rails in either DC or DCC.
The easiest and most practical way to handle a reversing loop in DCC is with a device called an "auto-reverser". These rapidly sense the momentary short circuit when the wheels span the gap into or out of a reversing section, and change the polarity of the reversing section automatically to match. Note that changing the polarity of the rails does not change the direction of the loco - that is done by the decoder inside the loco. To prevent confusion caused by reverse section gaps in both rails being spanned at exactly the same moment, it is recommended to stagger the reversing section gaps by 1/8" or more in DCC.
DCC problems with dirty track, voltage drops, short circuits, and the like have more visible consequences than with regular DC. You either lose control of the loco, or the layout shuts down (every block connected to a given DCC unit). I would recommend feeders for each rail in every one of your current blocks in DCC. A bus wire (at least 14 gauge in your case) should be run around the layout (but not tied together at the far end) for each rail. Feeders will attach to the appropriate bus wire unless you are keeping your block wiring. If you are keeping your block wiring, both rails must be controlled by the block switch. Your feeders would run from the block switches to the track.
yours in control