I've bought licensing so that either controller can manage the full complement of access points.
What I've found is this...
Some components of your configuration are syncronized between the controllers.
Some are not (public access web pages and attributes have to be manually syncronized if you've made any changes)
If you use guest access/web authentication, you must move your dhcp to an external server... (it's pretty straight forward). Address translation is a bit more obnoxious...
The Virtualized controller IP address uses the same mac address as the primary controller (which can cause ICMP connectivity problems - though it seems much better under later rev's of code)...
Things get broken out a little as far as where to go to configure what... I find I have to search back and forth between the team level configuration and the controller level... note that you have to actually connect to the secondary controller for some configuration changes such as the public access files and attributes)
The system tends to somewhat load balance access points between controllers...
I also found that I needed to make some changes in the egress for my internet access... I've placed my "Internet" vlan in a dmz and then address translate the out-bound connections on the campus ASA...