If you sign the check "For Deposit Only", the bank will put it in your account. You may need to set up a "payable name" on the account matching your DBA alias. However, having counted offerings for a church on several occasions, I know that banks simply have no choice but to be lax about the "Pay to the Order Of" line on checks. Say the church's "legal name" for which the operating funds account was opened is "Saint Barnabas Episcopal Church of Red Bluff". You'll get offering checks made out to "Saint Barnabas", "Saint B's", "Episcopal Church of Red Bluff", "Red Bluff Episcopal", "Youth Group Fund", "Pastor Frank", etc. The bank will take em all; just gotta stamp em with the endorsement for the church. Sometimes the money will be "earmarked" based on the payable line; any attempt to pay the pastor directly will go into his "discretionary fund", and anything payable to a specific subgroup of the church will go into their asset account line, but really all the cash goes directly to the same bank account anyway.
For-profit operations are similar; an apartment complex may get checks payable to the apartment name, the management company name, even the landlord. I expect that your freelance work will be no different.