This is an excellent question. I have 4 SW boxes, the primary SW server, a SW SQL server, a SW flat file server and a secondary poller. The update/restart procedure could be critical to "efficiently" maintaining these servers. I know the Configuration Wizard is almost magical, but a good procedure will save a lot of time.
Currently I:
There are services other than the main poller services that can be running and cause things to not return to service properly. I'd make sure everything on the services list is actually stopped manually as some things aren't stopped with "Stop all services".
I have used Solarwinds products for several years and only had the teams doing the patching reboot the servers when they were done. I just had them schedule the patches in chunks on different evenings so the whole system didn't go down at once. I never had a problem.