I'm no expert by any means, but I have watched ebay pretty closely over the last couple years as I've tried to build up my collection. And my observation would be that you will likely make more money by selling stuff in smaller pieces/groups rather than trying to list and sell as one big army/armies.
For example, if you are selling a Minas Tirith army, maybe list Boromir and Faramir together, then list the captains & banners together, then groups of 12 to 24 Warriors together, etc, etc....the main trouble with listing them all together as one big group is that you potentially limit your amount of prospective buyers because some people just can't afford a $200 lot and others may only want some of the pieces and don't want to pay for a bunch of stuff that they already have, you know ?
The only other advice I'd offer to you is to perhaps give it a good thinking over before pulling the trigger on selling. I'm very sorry to hear about your theft, as that's just awful, and perhaps you're just very discouraged at this moment (understandably so !), but think it over a bit and try not to do anything too rash that you may regret a bit later on...
Good luck with whatever decision you reach !