Hi Shane. This is generally frowned upon as you could potentially create a "death rig", i.e. if the line breaks above the shot, the fish could be trailing the method feeder and this could cause the fish to snag up and die. Without the shot, the feeder will be free to run off and the fish only has a bit of line to deal with.
I've borrowed this image from the ESP website that shows an in-line drop off system. The end of the swivel is plugged into the lead and will drop off with a bit of head shaking. The draw back and that it makes fishing expensive and the environmental impact of dumping fishing tackle troubles me.
If you are fishing a snaggy river with a lot of boulders, unfortunately you are going to suffer from the fish using them to escape. Rather than using a method feeder, you could use a lead and wrap the method mix around that or use PVA bags to create a feeding area.
Probably the best advice I can offer is to fish above the snags if possible and draw the fish out with feed. In rivers, you can't beat a bait dropper (below) to lay a carpet of bait down.