1999 3.0l doesn't have a distributor, they switched to distributorless in 1995
If you mean the Cam synchronizer housing that is now in the old distributor hole, then it will sit flush on the block, it does have to mesh with the cam gear AND then the oil pump drive below the cam, so once it is place you may have to move the crank manually a 1/2 turn in either direction to get it to mesh with oil pump drive.
It will then drop into place