Heres how I got the Auto Windows Up feature
to work with my trunk release button on my keyfob.

Here is how its done on an 07:
The motors are smart motors with the control modules for
UP/DOWN contained within the door panels. The
motor/modules are supplied 12V constant (LiteBlue C518)
along with a DACC or Accessory Delay power. You must
supply the modules 12V on the DACC wire when you
want the windows to be able to move, This is done either
with the alarm module 12V arming output or an off-delay relay.
The thought on this is to supply the DACC 12V requirement
for the windows to be able to move when you want them
to move (when the alarm is first armed). Either the alarm can
meet this requirement in the form of a timed output when first
armed of the required time needed to allow the windows to roll
up completely from the fully down position. Or a pulsed
output from the alarm when arming to trigger an off-delay
relay set to the required time. The colors of the DACC wires
are Red/LiteBlue for both the left and right motor/modules.
A diode should be used to prevent backfeeding of other
DACC controlled accessories in the vehicle. This is
connected at the SJB C2280G Red/LiteBlue wire. This requires
running a single wire from the drivers side door where the
relays are located to the SJB C2280G, the only oval connector
on the rear of the SJB.
The next requirement that needs to be met is the UP
and AUTO inputs to the modules. The UP is made normally
when the OEM switch is lifted to the first position making
the UP input and then the AUTO input is made in the second
position while maintaining the UP input. This can be
accomplished with a 4PDT relay. Hook the first set of NO
contacts of the relay to the UP module input (left side - White/Black )
and the other connection goes to 12V DACC connection to make
the relay sourcing. Then hook up the second set of contacts to the
AUTO module input (left side - Violet/LiteGreen) and the other
connection to 12V DACC connection to make it sourcing also.
The same needs to be done for the other side. (UP right side -
White/Yellow AUTO right side - Violet/LiteBlue). All the wires
can be accessed in the drivers door via C504 at the OEM power
window switch. 2 DPDT relays can also be used in place of the
4PDT relay if you cannot find one. Just hook the coils in parallel
and be sure to use a diode accross the coil for PIV protection.
Constant 12V can be obtained from the LiteBlue wire on C518
on the left front motor/module.
I verified operation of the above mod by using two off-delay
relays with one being set to the time required to allow the
windows to roll up from the fully down position and the second
one being a 4PDT set to a 1 second pulse to mimic the UP
and AUTO inputs to the left/right motor/modules. I used a diode
at the SJB C2280G Red/LiteBlue wire to keep other OEM
accessories hooked to the DACC wire from being powered
by my circuit. I then hooked up the inputs of the delay relays
to the trunk release output of the SmartJunctionBox and now
I can roll up my windows with the trunk release button on my
remote. Hmmm. 1 press = UP and 2 quick presses = DOWN?
I will be thinking about the circuit needed to do this. The addition
of yet another relay breaks the connection between the timer relays
and the trunk release output of the SJB preventing the rolling
up of the windows while the ignition is on. I should have just
used a 12V PLC and whipped up some logic for proper operation.

It can be done but its not for the weak at heart.