Yes our software supports multiple companies for the same price of $39. The software supports 1099 MISC reporting requirements for LLCs, so you should be fine.
As for electronic filing, the software supports IRS publication 1220 and allows you to create ready-to-file 1099 E-File submissions with the FIRE (Filing Information Retunes Electronically) system.
I suggest you visit the 1099 software page to download a free trial and see how our program works.
Real Business Solutions Support Team, Makers of W2 Mate and Payroll Mate
708-479-8731