To answer the question, it doesn't matter where the money is, so long as it's available to spend. This is because it's not actually savings; it's where your paychecks go to wait to be spent next month.
To answer the question I want to answer, what you're talking about is a concern that you won't let money sit. This is a skill, and a critical one for YNAB-ers. It's one of the keys to the security of having rainy day funds, emergency funds, and other designated reserves all sitting there, waiting to be spent. The idea is to get away from the illusion of security that physically 'segregating' money gives us (I say us because most of us have tried it and failed). Instead, you let money sit. Here's a link to a famous post by Patzer about letting money sit
I don't think I can add anything to that!
"It’s still all about the method. Fancy Cloud Sync algorithm aside...the software is there to help you become more aware (Rule One), anticipatory (Rule Two), flexible (Rule Three), and secure."--Jesse's blog, A Method to Your Madness