a decent exacto knife should be the only tool you need. i have done what ezrem said a few times before. use the xacto knife to release the pins from the plug housing and move them to a different slot. then cut off the extra plug. before you cut it off, hold the plug next to whatever you need to plug it in and see what the best side to cut off is.

it sounds like you have 2s (7.4v) batteries. the wires should be 0v, 3.7v, and 7.4v in that order on both styles of connectors, hyperion style just has a bunch of empty slots in it.