Biggest trick is that a) the automatic installer doesn't work, and hasn't for some time, and b) the manual installer does not use typical MCinfo setup. Instead, you must extract the files and copy the "put into mods folder"'s content -- not the folder itself -- into the mods folder, so that you have "Minecraft\instances\{Instance Name}\minecraft\mods\millenaire4.9.5.zip", "Minecraft\instances\{Instance Name}\minecraft\mods\millenaire" and "Minecraft\instances\{Instance Name}\minecraft\mods\millenaire\millenaire-custom". ((It can also help to delete languages inside "Minecraft\instances\{Instance Name}\minecraft\mods\millenaire\languages" that you don't use, due to how Windows handles language support.))
The default Millenaire settings /will conflict/ with Buildcraft in a modded Minecraft install (and likely will in a FTB install), so you will need to change the IDs on a handful of things, as standard. It may not spawn villages in mod-based biomes. Beyond that, it is do-able.