This is the “hard” part for coming up with a driver. There are some drivers that guys on this forum have made to separately control multiple LED emitters. Have a look around, especially in the Oshpark Projects thread. Also, if you give more specific information about exactly what you’re trying to accomplish with modes, etc. then you may get better help than me to come along.
One thought I just had about the beam/centering issue: Use either a triple or a quad board and optics. Then, each emitter will have its own focus, and the beam(s) will look fine. Dale (DBCstm) has been making some triples in an Eagle Eye X6 host and says it is pretty easy to accomplish. Others have started doing the same now. You can use one white and two reds or two whites and one red, depending on your needs.