What's the best way to manage two bank accounts on different sides of the country? Can I use Paypal?

I have one bank account in Minnesota, at a local credit union, and another in Connecticut, at a small bank that only has branches in CT. What is the best way to manage the two accounts? I have a debit/atm card for each, and the CT one refunds all my atm fees anywhere in the country. Is there an easy (electronic) way to transfer money between them? Maybe using paypal or electronic bill pay? Can I schedule a direct deposit into one account to automatically be transferred out of that account and into another one? Are there any disadvantages to this plan?