Best Practices Question

First background on my set up.

I'm the sole Desktop Admin for a company with right at 800 Machines. 9 out 10 of those are Desktops.
Little over 200 reside in my local building. The rest are spread across the country.
I have two larger sites with about 300 machines each that both have their own Distribution Server.

So Question:

How should I group these machines together? How many should be in a single scan, download, and deploy task?
Here's why I ask.
When running a single machine through the update process everything completes as expected.
When I run a large group 300-400 at a time I always end up with about a 50% completion rate.
150 to 200 fail some patch or another.