I'm a little fuzzy as to what you have done here... Am I correct that you have entered a bunch of conventional frequencies and assigned them to scan lists, then programmed a trunked system and added it to one of these lists? Shouldn't be a problem there. Just remember though, you don't really 'add' the trunked system to a list. The system is an object on it's own, and the talkgroups belonging to that system can be assigned to any of your scan lists.
As far as turning scan lists on and off, it couldn't be any easier. Press the 1 button to turn list 1 on and off etc etc up to 9. The 0 button turns on list 10. Then for 11 thru 20 press FUNC #.
If you aren't hearing any activity on these talkgroups make sure you have them assigned to the scan list that you think you do, and that list is enabled. Also watch the display while the radio is scanning. If it is properly receiving the trunked system in question you will see it pause as it scans the control channel and the T icon should light up briefly. This indicates the radio is properly receiving the control channel from the system. If you don't see that, then maybe you have a reception issue or perhaps the system is using a control channel frequency that you don't have entered into your radio.