1) You should not stop using your Cpap machine just because your nose is sore. You just do not want to do that kind of damage to your body. Short term, you can use over-the-counter decongestants such as Alfrin (no good long term, as nasty rebound effect). If you really cannot breath through your nose while it's healing, get yourself a full-face mask.
2) It's better if you can do without cortisoid sprays such as Flonase. Have you tried daily salt-soda nasal rinses? (I use the Neilmed packets with a sqeeze bottle.) However, if you do start using again, have your doctor prescribe something other than Flonase--there are at least a half dozen different ones.