Small Update: Finally managed to do it for some of the mods I'm trying to merge, including the ones mentioned above!
I followed this guide:
http://larian.com/forums/ubbthreads.php?ubb=showflat&Number=620801#Post620801 for loading third party mods on my machine.
Then I opened the Story Editor on that project, changed project to my mod-merge project, and right-clicked the white fields, selecting the option to add to my mod, which I assume is what you meant before?
A few of the mods, though, I seem to be unable to load following the method above. LeaderLib, for example. When trying to open the project, it says it is unable to do so, but the meta.lsx on the Mods folder for it shows no dependencies which I may be missing. Any thoughts on why that might be? Final piece of the puzzle for me here, I think!