Are you talking about Er9x or OpenTx/Open9x?
Both of them are flashed in the same way, need same hardware mods, but different software for flashing. So you can flash anyone of them, whenever you want.Open Tx has more options to play with, so is more advanced and complex as compared to er9x.
But if you are a beginner, start with Er9x, then if you feel the need try OpenTx.
Im using Er9x with Flysky 9x, and I dont even use half of the features available right now. Its really about your preference.But both of them are anytime better than stock firmware.Most of the data regarding the mod is available online, just gOOgle!
Read more here
http://www.rcgroups.com/forums/showthread.php?t=1266162