I am not sure why you have these two lines – they will always be false since they follow your HIGH and LOW statements ... delete them (in my opinion)

Code:
if outputline0=0 then outputline1=1 (these are the two lines i am having)
if outputline0=1 then ouputline1=0 ( problems with )
To get you going, try this for your Loop – Goto Loop section (written close to your style).

Code:
Loop:
'
'
'Test for Trigger
'----------------
If InputTrigger=0 then
	pause 30				' Debounce time
	If InputTrigger = 1 then Loop	' Debounce check – exit out of loop if not low after 30 mS

	While InputTrigger=0			' Wait for button release before updating
	Wend					' so you do not race through your Loop routine a zillion times before you release the button

	GPIO = GPIO ^ 3			' Toggle bits 0 and 1 - See PBP manual section 4.17.14
Endif
Goto Loop
After this works, you can work on saving the state of the toggle in EEPROM. What PIC are you using?