ultra start remote start, transponder unit

Have you actually read the install guide?  Don't take that the wrong way, it's just that each wire has a description, and an example application...in the install guide.

The aux bypass output IS used for your bypass module. All 3 wires.

1) Anti-Grind/Starter Kill - Negative Output active during remote start. 

alright, heres the info you need broken down. The negative output is used to energize a relay for many purposes - starter-kill, anti grind, bypass activation, rear defrost, etc. now, cheap units have either or options for starter kill or anti grind. good units should have both features, so make sure you program which is best for you(unless they offer both - which they should). you cant use a antigrind to do a bypass. it acts like an immobilizer so when you arm your car, no1 can start it with the key or even by hot wiring. starter kill is nice so no one can start your car while anti grind prevents you cranking again if you already remote started. you can use the negative output during remote start to activate a bypass, but no need because your unit has dedicated outputs for bypass modules (3 pin)  The negative output triggers a relay and breaks continuity on the start wire. if you wish to use it, heres how to wire it up.

85 - constant 12v

2) auxiliary Bypass connector (3pin White)  the WHITE/ violet wires are for Ground While Running (-) -250ma ground output while remote starter is active and Black is ground(-) 250ma ground output and Red is (+) - 250ma 12Volt output.  Can this be used for the transponder bypass as well?

yes this will be used to trigger the bypass module ONLY if needed when your vehicle has a factory anti theft system. most bypass modules require constant 12v and ground, but i suggest you dont use the red and black from that 3pin harness. just connect the bypass to the appropriate wires and use the WHITE/ VIOLET to trigger the bypass during the remote start sequence. hope this fills you in.

oh sorry if i didnt make it clearer =) i was tryin to say get power and ground from other locations insted of tapping off the unit.

exactley !