The number of MG3s in a German squad or company varies from branch to branch. In a true infantry platoon (Panzergrenadiere etc.), the standard was one MG3 per squad. The MG3 is always operated by a gunner and a loader. The loader carries a spare barrel and MG ammo. It was never used in the automatic rifle role like the M249 SAW, as the gun itself doesn't lend itself to that use. It's too heavy, too cumbersome to shoot well from any position but prone and off the bipod, and requires too many bits that come with it.
The German Army uses their MG3 much in the same way as the US Army uses the M240 GPMG.
The MG3 will not be replaced by the MG4, by the way. It'll still be used in its customary squad, and platoon-level GPMG role, as well as in the vehicle-mounted role. The MG4 is just filling the requirement to have a 5.56x45 squad automatic weapon that uses the same ammo as the new G36s. There'll be two MG4s per infantry squad, but they won't replace the MG3 because the MG3 was never used in the SAW role.