I've also got both sides of my 8800 identical, as it makes it easier to keep track of where things are. I seriously doubt I'll ever have a need to have each memory on both sides be unique. I've been using CHIRP and a $6 cable from eBay, and it's been working great so far.
In my case, I've been organizing the memories using "banks" (or groups) - not the actual memory banks on the radio though. These are basically little clusters of related stations. As the 8800 doesn't require you to have the memories be continuous, I start the different groups on numbers that are easy to remember. The main set of repeaters and frequencies I use are from memories 1-17. Then, starting at memory slot #20, are the repeaters that belong to the Intermountain Intertie system, which covers most of Utah and Idaho. Slots 40-45 are a different repeater system, and 50-57 are the various NOAA weather stations. And so on… Basically each group starts on a multiple of 10.
I've also got the actual memory banks setup, but I've just found that it's easier to not have to switch into the memory bank mode, and just leave it in memory mode. This way I can just use the keypad to jump to the starting point for the group I want to use.
I've got the hyper memory buttons setup for a couple of different scanning scenarios, and I bounce between then often. One will scan all of my memories. Another scans a smaller set of preferred memories, just the top 10 or so I use. I've also got one setup to jump directly to the weather bank for a quick check. In the cases where I'm scanning, I've almost always got once side of the radio locked to either 146.52, or one of the more popular repeaters here in town.
Best advice I can give though, is to just play with it. Start using it, and eventually you'll find a system & setup that works for you.