Trunked systems are handled independently from scan lists. You can scan as many trunked systems in one scan list as the scanner can hold, but each trunked systems handles sites based on settings. This still applies if you were to split one trunked system into several different scan lists by splitting up the talkgroups.
From what you want to do, you might want to check out the Multi-Site settings for each trunked system if you are monitoring a Motorola or P25 system.
Here is a link to the description in the Easier to Read Manual. Setting it to Stat(ionary) mode will cycle a trunked system through all the control channels that are programmed for a system.
An alternative is that you can duplicate trunked systems and the talkgroups you are scanning, then place them into the same scan list in order to force the sites you want to scan. The downside of this is that it will take additional memory since you have to duplicate everything.