Hi there, I am fairly new to YNAB, so forgive me if this is wrong, but it seems like YNAB could be used quite nicely for small business alongside small business accounting software, even if you are accounting on an accrual basis, as long as you were importing your transactions from the accounting software (e.g., using a CSV file -- I use Xero and I can export my data in .csv file), rather than importing transactions from your bank statement. Then everything would be in sync.
Just an idea.
Whoops -- just realized that due to YNAB's limitation in not being able to have multiple income categories, this might not work if you have multiple income categories in the accounting system (as most businesses do). This seems like the Achille's heel of YNAB for small business.