As far as I know, tax advantaged accounts: cash in, cash out. Internal Revenue Code Section 219(e)(1) specifies cash...which means those REITs, bonds, etc need to be sold in your taxable and bought in your tax advantaged. There isn't a magic way to do an in-kind transfer.
Depending on the amounts, unrealized gains, time to retirement, etc, etc it may or may not make sense to sell+buy to "optimize" your accounts. It really depends on the specifics of your situation.