I think as long as the only things flowing in and out of the designated fund accounts are restricted activity, this will work great. My suggestion is more for folks who have only a general fund bank account, but need to track how much of that bank balance is actually donor-restricted/donor-directed. 

Another thing you will need to think of is how to keep the revenue and expense side of the bank activity separate. For GAAP accounting, restricted fund activity has no impact to the Net P&L - as Restricted Funds are used (expense), you would recognize the revenue at the same time, so the "net income" impact is 0 to P&L. That being said, if you're not doing GAAP, I'm not sure that matters as much.