Probably should head on over to the official team cyclops web site, teamcyclops.com and either download v1.22 of the firmware from the support page or 1.3B3 (look in the beta firmware forum, stickied topic for link). Download the manual and READ it while you're looking at the support page as well, and moonshell(see below).
The beta fixes some games that had problems with v1.22, and also lets you use the realtime save feature if you want/need it for some reason. You have to enable realtime saves in the setting menu, and hold SELECT plus A IIRC when you start an app to enable RTS. I believe that it asks you even then if you want it enabled. Same for cheats, you need to select enable in the settings menu if you want cheats enabled for games that have them.
If none of those apply, you should probably stick with v1.22 as it's the stable firmware release.
Also download the Evolution version of Moonshell from the support page, unrar the archive and copy the resultant moonshl directory to the root of your uSD car ID you want moonshell on your Evo.
That's about it. ROMs install by dragging and dropping them to the uSD. Homebrew put anywhere that you like unless the homebrew install instruction instruct you to put it in a particular location, also pay attention to whether or not they tell/suggest that you create various directories.
If you go download DS Organize 3.2final from the author's page the archive includes a folder that lets you use DSO instead of moonshell on the Evolution. (Comes with a specially created moonshell folder that'll launch DSO instead of moonshell.) Personally, I just use the Evolution patched version of moonshell and load DSO separately.