Should I pay quarterly taxes as an Individual, or as my Single Partner LLC?

I have a Single Partner LLC, which has its own EIN etc.

All of my income is from the LLC. I pay my taxes as an individual using my SSN. I have been filing and paying my quarterly tax pre-payments as the LLC and using my EIN, but then the IRS told me they cannot connect those payments to my annual tax filing.

I've now changed over and file my quarterly taxes as an individual using my SSN. 

Is this the right thing to do?

Should I do the same for my state taxes?