Can I leave the cart attached using cd method if I demag after?
No you have to detach the cartridge leads. Either use an adaptor aka the Cable Cooker or you can fashion your own. (I used to solder alligator clips that I bought at Radio Shack to either end of a piece of wire.) Then unscrew the RCA barrel on the IC and attach one alligator clip to the + and attach the alligator clip to the cartridge lead. Then do the same thing for -. Then repeat for the other channel. You may just want to make sure wire is supported so it doesn't put any stress on the cartridge leads. You can even use say a break-in CD on the tonearm wire if you desire.
The phono doesn't need to be on.