'97 Jeep Starter Motor

Okay..a real quick question here.
My starter just went dead on my 97 jeep wrangler, I got a heavier duty
one (A mean green) but the problem i am having is that the wiring is
different. The wiring to attach to the starter is not two wires..well
it is..but its that the two wires are molded together using ruber or
latex.And the orientation on the stock motor is so that both terminals
are vertical and accordingly, the wiring "boot" is oriented so that it
will only fit that way. Now, on the new motor, one terminal is vertical
but the other is horizontal. So, i need to know if i should just try
and serperate the two wires by just cutting the boot or if there are
any other suggestion?

thanks.

I hope i made it clear enough