Hey @HannahVicary,

Welcome to the community.

I am not well-versed American corporate law as it pertains to parent companies, affiliates and financials. That's a legal question I'd seek legal advice on, just to make sure. 

Now, you can absolutely create invoices with different logos in QuickBooks. All you have to do is create and save multiple templates. It's not uncommon for the same business to use different invoice templates (styled and organized) for a segmented client-base. 

Again, regarding accounts and draw between different LLCs, seek legal advice and stay compliant!