The best place, in my opinion, is under the rear passenger seat, tucked under the seat. I made a UHMW mounting plate, mounted my 700 watt 5 channel JL marine amp on it, and then tucked it up under the seat and mounted it with about 7 zip ties to small holes I drilled into the lower seat frame apron. Fits perfect, is shielded from spray and is the closest location possible to the battery. Over 600 trail miles through mud, water and dust with no issues. It's also in an easy location to tweak levels and make adjustments.
I had my rockford fosgate m400 in the glove box. It died first time I hit a water hole. Really depends on what you plan on doing. If you're gonna be in mud and water.... I'd mount it as high as possible and build it into a sealed container.