Yes... you can have separate 2s and 3s packs but that means you have to charge two times.
You will be much better with a 5s charger.. or you can buy another charger like yours so you can charge both at the same time.
I have a few pic of my truck... in this thread
http://www.rc-monster.com/forum/showthread.php?t=5572 check post#14
but I need to get some new ones... maybe I can do that tonight.
Jammin CRT MM/Neu 1515 1700kv
Losi 8IGHT MM/Neu 1512 1900kv
Kyosho 777
T4 MM 5700
B4 LRP
XX4 MM 7700
old losi xxcr, MM4600 4s lipo 70mph+