Are either of these accounts IRA's, or is it all in taxable? Generally speaking, you'd want bond funds in tax deferred accounts while keeping taxable as tax efficient as possible, though with munis that may not be as big a concern. Given that, I see two concerns:
1.Tax loss harvesting. One of the key features of Betterment, you can run afoul of the wash sale rule if you're managing assets in multiple places and its algorithm doesn't know your full holdings. Maybe not a big deal, depends on what you plan to hold in each.
2. Rebalancing. Personally, I choose to hold my largest asset class by far (total US stock market) in my taxable, while holding that class and any others in 401k/IRA. That way, if I need to rebalance to target asset allocation, I can do all of the rebalancing in tax deffered accounts with no taxable events. Since my taxable account is the smaller, and total US is the majority of my portfolio (would be 100%, but my best 401k option is a vanguard target retirement fund, which holds some international), I'll never get to a scenario where I have so much VTSAX in taxable that I cant rebalance without selling in the taxable account.
