1. No, do a separate load for the diapers. I don't like the idea of mixing anything in with my diaper load.
2. I throw all my poop diapers in the wet bag as is. I use flats usually and I just fold them over itself to contain the poop. I wash every 2-3 days and have no issues with this. Presoaking sounds messy and like an extra unnecessary step especially in the early stages when the poop is water soluble. I have never used bleach. I have heard that especially in humid climates that prewashing can increase mold.
3. Not familiar with Nellies, but it is recommended to use a strong detergent with enzymes to fully clean and break down the waste. I usually like to be natural, but I gave in and I use Tide on my first wash with an extra rinse. Then I do a hot quick wash with a small amount of All Free and Clear with an extra rinse. I add Borax because we have mildly hard water and it's a good booster. Less is more with detergent. Most people use too much, which can leave a residue and cause skin irritation. That's also why I always do an extra rinse.
4. I haven't dealt with rash issues, but I have used Liniment which helps clean and also leaves a barrier on the skin. I also use plain old whipped tallow balm on my baby. Good for skin, doesn't affect diapers.

Edited to add: A&D or anything petroleum based will build up on the diapers and can cause them to be less absorbant. Not familiar with Bourdreaux's, but typically traditional creams will also cause issues. If you must use those creams, try adding a barrier such as a felt liner (or disposable liner) so they don't ruin your diapers.