It's really what you're used to doing I suppose, but I prefer installing and tweaking 3.9, and a small partition with bare 3.1 for test. Recently, I installed an '030 card in my desktop 1200 for test (it's normally fitted with an 80MHz Apollo 1260), and I was amazed at the lack of slowdown in 3.9 compared to the '060 - no problem here with speed. My bare 3.1 install boots maybe a second or so faster.
