I hope this will answer both of your posts. If you are still confused, just ask and I'll try to make it more clear.
Start by creating an "available for building" Loose Part list for each large set you will be using. For example label one 42009, another could be Uni-mog or whatever other large set you own. 2 or 3 small sets could easily be combined into one list.
Use the part out feature on the Set Home Page to put the parts from each set in the correct loose parts list. Once you have parted out the set, you need to manually remove the set from your Set List. Otherwise you will have a double count of the parts.
Edit-After you have all the parts in the loose parts lists, you need to go to the Build tab at the top of a rebrickable page.
It will give you options to check off. Check only the "my parts list" box.
Then set the match bar to exact.
At the bottom, click the Find Sets to Build button.
This will give you all the sets with 100% in your loose parts list.
Choose the one you need and click on it.
This should bring up a page that says
"You are able to build this set from your loose parts collection." There will be a link for Combine these parts.
When you build an MOC with the 100% combine link, you can choose the loose part list you want to start with, and the parts will be removed from that list first. After that parts will be removed from other available part lists until the 100% is reached. The MOC will appear in your chosen Set List.
The remaining parts from each set you parted out will be in their own loose parts list, ready to be used for other MOCs. If you wanted to combine all these left-over parts into one list, create a Total loose parts list. Export each separate left-over list to your desktop, then go to the Total loose parts list and import each one using the APPEND button. Once you have added them all to the Total list, be sure to delete each left-over list and all its parts so you don't have a double count.
If you wanted to put the 42009 set back together, you could part out the MOCs you built into their own loose part list, remove the MOC from your set list, and then use the "build this set" to get the 100% link for the 42009.