I would use two remotes not one.

And use the same remote in each zone. If you were to use a different remote cin each zone you would be creating more programming work for yourself and more importantly handing your customer remotes with two different interfaces.

And don't sell a remote that you can't program with a laptop. MX450's are for DIY guys and over the counter retail customers, period. And for anyone out there that disagrees with me, you need put on your big girl panties and work on your remote control sales pitch.

As far as the MRF350 goes it depends on your clients needs and the wiring. If they are going to be using the two zones at the same time then I would say to use two MRF350's. If they are not going to use them at the same time you could get away with using one of them and splitting a couple ir outputs.