Hello Charles.
The problem is that Workspaces don't sync. It's the MLO file that syncs. When you create a workspace, it's just another view into the same file. The new Workspace duplicates the previous one until you use a different filter in it.
It sounds like what you're trying to do is to look at different MLO files. To do that, you need to set up a new Profile on your iPad. (Profiles are accessed by tapping on the gear-wheel "settings" icon at the bottom). However, if you're going to be working in different profiles on the iPad, each syncing with a different file on your desktop, you're going to have to be extremely careful to make sure that you never sync with the wrong file. In MLO, it's devices (iPad, PC) which sync, not files - This means that when you change profile on your iPad, you'll need to remember to open the other MLO file on your PC. It's very easy to get this wrong and end up syncing with the wrong file, creating a massive, merged file of the two.
If I've mis-interpreted what you're after, feel free to post a reply and I or someone in the group will try to help further.
Stéphane