Rental property expenses

If you are a single member LLC, you are a disregarded entity for tax purposes, and will file the LLC's rental properties on Schedule E as part of your personal tax return.  Since you are an LLC, you should indicate so.  It won't change your tax liability, but it's something asked on the tax return.  As for expenses that are combined on the same invoice for multiple properties, just split the expenses between the two properties in a manner that makes sense.  

Keep in mind that @DavidD66 is assuming that you have chosen the default entity as a single member LLC (disregarded entity) and have not elected to check-the-box to be an association taxed as a C corporation or an S corporation.

Absolutely nothing what-so-ever concerning your long term residential rental real estate income/expenses will be reported on SCH C. All rental income/expenses is reported on SCH E. Therefore, on your tax return you have no need to report your EIN, as there is nowhere on the SCH E to enter an EIN.

Also, some of the expenses were combined on the invoices by the property manager as the properties are neighboring. How do I report these expenses?

You can split them as best you can. Just be reasonable. For the future, let your property manager know you need separate documentation for each individual rental property. This should include them providing you management fee billing for each property separately. Makes your life easier at tax filing time.

Also, talk to your property manager about how they're going to handle things at tax time. For example, with the 1099-MISC they issue you be for *ALL* rental income? Or just the rental income they pay to you minus their management fees, maintenance costs, repair costs, HOA fees, etc. ??  If the latter, then they need to provide you receipts or a detailed breakdown that accounts for every single penny they spend on the properties.