Once you have filed for the LLC name, you now also need to obtain a Tax ID from the IRS for the LLC. Once you have obtained the Tax ID, then you also need to draft the Articles of Organization which should explain the purpose of the LLC and the members if known, the registered agent. See: http://smallbusiness.findlaw.com/business-structures/llc/forming-llc-articles-organization.html
The articles of organization and the tax ID need to be filed with the Sec. of State to obtain your LLC and as part of that filing you would also request a "ficticious business name" or DBA for the name of your store from the Secretary of State. Normally, the only other permits you need to operate would be those issued by the City of Indianapolis which would be applied for at City Hall.
Once the Articles of Organization are filed, then you would also draft a membership agreement/bylaws
(this does not get filed, but it governs how the membership will work, especially in event of divorce).
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