Yes, you can ask IRS to direct deposit your 2006 refund into one account, or split it among two or three different accounts. The choice is yours.
If you want your refund deposited into one account, use the special direct deposit lines on your tax return (Forms 1040, 1040A, etc.). If you want your refund deposited to two or three accounts, use Form 8888, Direct Deposit of Refund to More Than One Account.