Hello MacWilly,
Almonds would normally be trees. Whenever you prune, you introduce the possibility of infection, so only do it if you need to. There is an adage that you shouldn't prune unless the branch is small enough to prune with secateurs. That way the wound will be smaller and will heal more easily. Also, almonds do get silverleaf so don't prune until late summer. Always use sharp, clean implements, and disinfect them before you move onto your next plant.
As for what and where to cut - if you have two 'leaders' (two branches sticking up at the top) you can take out one. Make it the one that comes out of the main stem lowest down. If they both come out at the same height cut the thinner one. Don't cut flush with the main stem. Make the cut just beyond the branch 'collar' - you'll have a tiny bit of the branch left sticking out from the main stem. This should heal over well.
I hope your almond grows well and does you proud. They are lovely trees.
Emma
gardenersworld.com team.