The  separate entity is usually a sole owner Limited Liability Company or what is commonly known as a LLC.

The LLC is formed under the laws of your particular state with your IRA being the owner or member of the LLC.

Essentially, a sole owner Limited Liability Company is a hybrid entity.
If you are doing research into self directed IRAs, you're going to come across the terms "Checkbook IRA"; "Checkbook Control IRA; "Checkbook IRA LLC"; "Self-Directed IRA LLC"; or various combination of those terms.

All of these terms really refer to the same thing.  The "thing" is a separate entity that is formed to control your self directed IRA assets, whether it be for a traditional IRA or a Roth IRA.

How To Set-up a Checkbook Control IRA LLC

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Is a Checkbook IRA LLC Legal ?

The Tax Court seemed to say that it would be legal to at least initially fund an IRA owned entity, like a LLC.  However, subsequent funding of the LLC was not really discussed. 

You should also know that Tax Court cases and IRS Field Service Advisories are really at a fairly low level of importance.  Higher Court decisions and IRS Rulings carry much more weight.

The IRS may some day crack down on IRA LLC issues not specifically ruled upon in the Swanson case.   As IRA LLCs become more common, you can rest assured that the IRS will be paying more attention to them.

The important thing you should know is that a Checkbook IRA LLC can be very complicated.  It would be very easy for an IRA owner to become a little careless and inadvertently participate in a prohibited transaction -- which could become very costly.
The IRS has never made a clear and and exact ruling or statement as to whether a Checkbook IRA LLC can be established to control and to invest your IRA assets.

Those who support the position that an IRA LLC is legal, point to the ruling in the 1996 Swanson tax court case (Swanson v. Commissioner, 106 T.C. 76).  The Swanson case is very complicated and involved a foreign sales corporation, not a LLC.
It has the characteristics of both a corporation and a sole proprietorship. The corporation limited liability advantage is also enjoyed by the LLC. 

In general terms, "limited liability" means that the extent of liability and risk to an owner is limited to the amount of the owner's investment into the entity.

To start the a Checkbook IRA LLC, you first must have your IRA assets in a self-directed passive custodian IRA. A passive custodian must be IRS approved and would have to allow the investment of your IRA assets into the new LLC.

To put assets into a passive custodian IRA, you could make a direct transfer from a traditional or Roth IRA to the new passive custodian IRA.   You also could rollover a 401k; a 403b; a SEP-IRA; a self-employed retirement plan; or any other qualified retirement plan into the new passive custodian IRA account.
What Is a Checkbook IRA LLC?
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Is a Checkbook IRA LLC Legal or Not?

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There has been some controversy as to whether the establishment of a Checkbook IRA, LLC is in violation of the IRS prohibited transaction rules that apply to all IRAs.
You then, as manager of the LLC, would direct the passive IRA custodian to invest a portion or all of the IRA assets into the new LLC.  The IRA assets would be deposited into a LLC owned bank checking account.  You would now have control of the LLC checking account -- hence the term Checkbook Control IRA, LLC.

You now are able to invest your IRA into many types of diversified assets as long as you don't violate the IRS prohibited transation rules.    

It all sounds good and simple, doesn't it?  Well, unfortunately it isn't -- please read the following.