Yes, I use Total Modder now for Full Monty and as noted, all content across all TFM packs which is not in "#DBW" folder must be packaged separately in its own jsgme folder, and activated via GME. Thus as noted, you activate one pack in JSGME (I call mine "MONTY ROOT" which contains all stuff outside "#DBW" across all the Monty packs - I simply navigated though each monty pack and cut out all non #DBW content and pasted it into my MONTY ROOT pack), and then once that pack is active in JSGME, I load up Total Modder and activate my TFM profile. NOTE, in your TFM packs all the content outside #DBW directory should also be deleted from all TFM packs (you have that stuff in MONTY ROOT and activated via JSGME). Thus, your TFM packs would only contain "#DBW" and "documentation" folders.
As a refresher here is the post with screen shot of my setup using the GME/TM combo to load TFM quickly and efficiently.
There are some other tweaks like creating the separate "MONTY INIS" folder which contains the ini files per highest pack numbers (rather than storing iterative duplicates within each progressive pack), but this is for more experienced config tweakers who want to tidy up the set (sounds though like there are a lot of tweakers using TFM!).
Note, a key reason I use TM is of course speed in ability to switch from say UP3 to DBW TFM, or better..., from DBW 1916 to TFM (literally less than 2 minutes). I can fly a few of Monty's excellent WWI DBW 1916 campaign missions, and then easily switch the same code base over to TFM to fly with AVG in Burma all within the same hour, spending much more time in the virtual skies as compared to watching "paint dry" (2.5hrs+ on my rig when I used to switch using GME) as TFM loaded traditionally in JSGME.
~S~
wind
PS: one additional tip: If you use TrackIR for 6DOF, and switch between say 1916 or UP, etc... in GME, and TFM in TM, be sure to reset the Total Modder Executable Selector by opening the dialog and saving. I have found that when I run say, 1916 via GME using the SAS selector, and then decide to go visit TFM via Total Modder, I have to reset the TM Selector to get 6DOF to work. Not a big deal, just one step to do if you get into TFM via TM and find that 6DOF is not working (of course also sure Shift-F1 is not set).