When you create a manual check batch, are the transactions Payments or are they Cash Invoices? If Payments, then everything should be identical to printing checks via the Print/Post Checks and Advices function.

If you are entering Cash Invoices, then there is a different detail section type that is required for your check specification. It is the 'Advice body - Cash' section that prints cash invoice distributions. This is different than the 'Advice body - detail' section that prints paid invoices for Payment checks.

If you want to use the same spec for printing cash invoice-related checks as for payments, then both detail sections need to be on the spec. Ensure that the section height of the 'advice body - cash' is the same as the 'advice body - detail' so that the formatting remains the same. And you can only use the 'G codes' for printing information in the advice - this will be information such as the distribution code, GL account, description and tax information.