If I have money sitting at self directed IRA + checking account, can I invest in same property (commercial multi family) using both accounts?

How will it work from an llc perspective. If I keep property under an llc, will these be treated as separate shareholders? 

Charanjit,

it is possible in some circumstances to co-invest personally with your IRA but since you are considered "disqualified person" to your IRA such transaction might be prohibited. Be sure to speak with experienced professional who can give you guidance. Remember, advice you get on the internet will not count if IRS determines that you commuted prohibited transaction, but attorney's advice you can rely on. 

No, it would be a prohibited transaction--

Internal Revenue Code Sections 408 & 4975

Thanks @Dmitriy Fomichenko and @John Akolt Can I invest with other shareholders using my self directed ira under same llc?

I was advised by an attorney that I should not have my IRA invest in any property anywhere near where I personally own property because of the possible perception that the IRA was creating value to me personally.

It is possible to have your IRA invest into a property with other people. I have an investment in a mini-storage where my IRA owns one unit and other people and entities (including some other IRAs) own other units.

@Charanjit Singh

I believe it is allowable under certain circumstances to invest with your IRA. Reference the Swanson vs IRS case and you will see that the IRA account holder was actually the manager of the LLC of which his IRA was the member. This is the landmark case that created checkbook IRAs that many people mention in the BP community. Also the Adler decision talks about disqualified persons (specifically family members) and IRAs being commingled in investments. I personally think that, done correctly, partnering with your Ira on a deal is safer than checkbook IRAs.

Work with attorneys that understand these matters not many CPAs or Attorneys have a grasp on SDIRAs. 

If you pursue this partnering with your IRA understand that at a minimum:

any loans need to be non recourse. 

Pro rata share based on contributions to the project must be maintained from the beginning and throughout the venture.  

Both you and Your IRA must be able to do the deal without the other.

Neither you nor the IRA has a benefit as a result of the arrangement.

Yes, usually you set up an llc entirely owned by your self directed ira.  That llc joins as a member of the llc with the other 3rd party members.  You can manage your llc but you can't participate in it--no painting, remodeling, etc.  The penalties for screwing it up are severe.  If it is a grey area pay someone (through the llc) to do it and avoid the stress.  Ask an attorney/cpa until you have some experience with the boundaries.  

@Charanjit Singh

Yes such transaction is allowed provided specific rules are followed. You will want to work with a qualified professional  (e.g., CPA or attorney) on this type of transaction. 

To give you an idea, it can be done under a LLC where you pool your personal and IRA funds.