How do I set up bank accounts, etc., under a pen name?

Yes, I have, though not with a pen name.

Remember, when you open a joint account, you’re only required to provide one SSN. For instance, I opened a savings account with my daughter. It’s under her SSN, so the income is reported under her name. Same for the joint savings account with my wife. Only one of us gets the interest reported.

Thus, with your own legitimate SSN, the bank and IRS don’t care about the SSN for others on the account.

But it would be simple to fill out an account form, use both your own and your pen name, and hand it in to the teller. If they object, you can fill out your part, tell them that the other person is outside, then return five minutes later. It’s highly unlikely anyone would question you.

Will this get homeland security scrutiny? Probably not. As far as the bank knows, there are two people. And there is no law against using a false identity as long as there is no intent to defraud.

No need to indorse the check with any name.
Just “FOR DEPOSIT ONLY” will work with tellers at my local branch.

This would be harder to do these days than it would be to do even a year ago. My wife works for a bank and they are cracking down hard on poof of identity regulations. Their mantra is (apperantly) track the money to it’s source. It has made her job more difficult, but I suppose it protects the bank from fraud.
Disclaimer for the below:
I am not your financial/business advisor and the nothing in this post constitues finacial/business advice. Follow any advice at your own risk and consult your own licensed finacial advisor before making any decisions about what is best for you.

The easiest thing to do would be to incorporate and get a DBA or fictitious business name, do all your work through your corp and have all checks made payable to your corp. The (potential) additional tax benefits of incorporation would make this (likely) the most appealing option. (For example, corporations don’t get 1099’d.) There are other complications that would arise such as the corporation needing to loan out your services, but all of that can be taken care of by a competant business manager if and when you decide to do this.

I had a client who couldn’t use his real name for SAG reasons and this worked just fine for him. Though he wasn’t activly trying to hide his identity, so the situation is a bit different I suppose. It would be very hard to totally obscure your identity from anyone who really wanted to find it, but I suspect that most people won’t try too hard.