For basic troops (on both sides), use industrial equipment (i.e. 20% mass for internal structure, civilian armor that lets anything doing over 5 pts damage roll on crit table, etc)
Hand-held weaponry to simulate rocket pods on Mechs, or a Zentraedi's side-arm
For officer (aka hero) armor/vehicle, you put in the real BT gear (10% mass for internal structure, true armor, etc).
Fuel Cells (and Zentraedi equivalent) for regular troops, and actual fusion (Protoculture) reactors for the hero units.
I'd give the Zentraedi forces slightly more armor per ton, and their weapons do slightly more damage per ton to keep them a threat. Even if the players manage to defeat and steal Zentraedi gear, the armor will eventually get shot up, and Zentraedi weapons will eventually run out of ammo (or the lasers can't be maintained any more).