All IRA’s must have a custodian. There are many different types of custodians that allow you to have a self directed IRA LLC and how they allow payment.
Some custodians force you to send them any and all investment ideas for them to review and approve. If they approve it, they will purchase the investment FBO (for benefit of) the IRA. These services do not come cheaply however.
Another type of custodian will allow for a self directed IRA LLC but will only allow you to purchase investments they represent. This flies in the face of self direction.
The third type is a passive custodian and they allow for true checkbook controlled IRA LLC investments.
Depending upon the custodian you choose, they will regulate how you pay their fees.
At sdretirmentplans.com we utilize a passive custodian. Our clients can pay the set up fees for a self directed IRA LLC two ways. Some of our clients wish to write a check while others want to pay from funds inside the IRA. We work with our clients to calculate which is best for them. This can make a big difference over time especially if it is a Roth IRA LLC.