Better suggestions will come if we can see photos of what you're talking about. Have you ever hired an interior designed who worked with a blindfold on? We're blind folded here. Pix please!

Totally. Haven't moved furniture back up yet so I don't have a picture. Just didn't know if it's an odd choice to put a small circular rug under a desk chair under a larger desk--you know, like how it's standard advice to say to get a larger rug for your living room or one that fully fits your dining room chairs when they're pulled out from the table...I wanted to be sure I wouldn't be committing a design crime or something!

You have a beautiful space, by your description! I hate moving chairs on a rug unless they’re designed to move. Decide what’s important to you and find the furniture to fulfill the need. Your beautiful desk should drive the design.