Flan's mod requires a special
install procedure if I remember correctly. First you have to install the base mod (which could be done through the launcher), then run and close the game, then place the content packs in the Flan folder it creates. Unfortunately I think this needs to be done manually.
You'd then have to take care of any ID conflicts in the config (and consider doing a pastebin or posting the configs you end up using for others who want to do the same, if it doesn't violate the mod's TOS).