The hardest thing about installing mods for Torchlight 2 pre-guts is knowing where your PAK directory is.
it will either be in 1 of the 2 following places, For RUNIC downloaded Torchlight 2 it should be:
C:\Program Files\Torchlight II\PAKS
for STEAM downloaded Torchlight 2 it should be: (either x86 or non x86 depending on your 64bit?)
C:\Program Files (x86)\Steam\steamapps\common\Torchlight II\PAKS
I have the steam version, the steam directory is a direct copy and paste, and the RUNIC is second hand information. Now, once you locate that PAKS directory, and you have SYNERGIESV142.ZIP.. you USUALLY can double click the zip file, whever ever you downloaded it.. and a window will open with TWO PAK files. a SYNERGIES.PAK and a SYNERGIES.DAT.PAK in most cases you can select these two files (ctrl-A) and simply drag and drop them into your PAK directory.. if the files are already there, OVERWRITE. and you are done.
conversely if you don't understand drag and drop proceedure you could unpack them anywhere you want, and copy / move them into the pak folder already unpacked.
your main goal will be unpack the zip file, then put the data.pak and the .pak files INTO the PAK directory. without those files, you have no mod.