No links - I'm fairly sure everything you need is in the download section on this site, I'll just name them.
You will need either Rudolph's 3in1 Tool, GBALdr or NDStation to flash games to the 3in1. 3in1 Tool and NDStation both support running games from PSRAM, which is a fast and effective solution to run games under 128mbits. You can read more about them in various threads or websites, however it is generally recommended you use Rudolph's Tool for the best overall package, or if you want to support one of our very own (chuckstudios), use NDStation, which packages a GBA rom into an NDS rom. GBALdr supports skins, so you can make it look pretty. The choice is down to you in the end.
That would be pretty much all you need. There is an IPS patch for the 3in1 easily found stickied on the Sosuke forums, same with the rumble patch.