I'm not sure I understand your question, but I do most of my sales online.
The e-commerce option in SBA is just integration with eBay. It is pretty
useless for other online services. I use different software to manage my
online inventory and SBA to manage my bank account, print out invoices, etc.
I manually enter online sales as "Cash Sale" in SBA and export to Word so I
can print out a customized receipt to include in the package. The email
invoice is a nice option sometimes too. But everything is manual, requiring
extra steps and updating two databases.