1.Since I will be using this in a mobile type setup, will unplugging the 990 delete all my presets or are these stored no matter what the power setup is? I will be using this mostly on weekends only.
No. As I recall, the 990's settings persist even through prolonged power outages.
2.I will be using the Mackie as my only sub. On the Mackie there is a left and right input. I wanted to use the XLR cables. Will this work with only one output to the sub and will I lose any signal with only one input being used?
It depends on the sub, but typically you can use just the left channel input on the sub.
3. The powered speakers I am using have LED warnings on the back to monitor input signal. In a DJ or band application, these can be monitored. In my setup I do not have a clear line of site to the back of any of my speakers. I have read the setup guide in the instruction manual. I was wondering if using a Behringer XM822 to monitor the gain levels to basically be an alarm in the rack case in case anything changed would be a good idea. Basically it is a 100.00 mixer protecting 2000.00 worth of speakers. Any opinion on this?
Not sure on this one. If you plan to push them to levels that might lead to problems, it might be good to have something in place.