They will be fine. the 5th and 6th wires are just centre taps. They can be left unconnected but insulated. You wont loose any torque.
from the wiki
Quote
"pair" wires on 6 wire motors
On six-wire motors you'll find two groups of three wires in which all three wires are electrically connected to each other. These wires are connected to the same coil, one in the center of the coil, two at their ends. Accordingly, two of the possible pairings have a lower resistance, one pair has a higher one. Take the pair with the higher resistance and ignore the third wire.
The no-ohm-meter method can work here, too. Expect not two, but three stages of turning resistance. You want the two pairs which give the highest turning resistance.
After you found out which two of the six wires to ignore (one in each group), you can proceed as if you had four-wire motors.
