Married couple with TWO separate LLCs, How should we file?

Even when you have two separate LLC's it is almost always best from a tax standpoint to file as Married Filing Jointly.

See this TurboTax support FAQ for filing jointly versus separately - https://ttlc.intuit.com/turbotax-support/en-us/help-article/taxation/better-married-couple-file-jointly-separately/L338QHg8G_US_en_US?uid=lp8wgxpa

When filing jointly, you simply include separate schedule C for each business.  Turbotax can handle multiple schedule Cs attached to a single joint 1040.  Make sure the correct name and EIN are attached to each schedule C, and that you list the income and expenses to the correct schedule C.