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Payments from bill.com downloaded as a lump sum base on your daily transactions. With this, I'd recommend contacting our Customer Care Support to check if payments can be download as one or in batch.
Lastly, here's a few articles you can read for ideas about how you can manage your vendors and expenses: Income and expenses for QuickBooks Online.
If there's anything else that I can help you with, let me know in the comments always around ready to help.