Should invoice nos follow a sequence back to back ? If my 1st invoice is no 1001 and my 2nd no 1003, why ? will a payment be allocated the next in line doc no ?

Hey there, @moniqueh1905-gma.

QuickBooks automatically assign numbers to your sales forms. The program will also create a sequence to easily track your transactions. 

Since your first invoice is no. 1001, then your second transaction should be 1002. It could be that someone has created this invoice yet it was deleted after creating the third one. This can be the reason why your next invoice number is 1003 after invoice no. 1001.  

To check, you can review your audit log. QuickBooks Online keeps track of your activities using this feature. This will help you can see who made changes to your books and what they did.

1. Sign in as an admin and go to Settings, then select Audit Log.
2. Click Filter and use the fields on the Filter panel to choose the appropriate User, Date, or Events filter to narrow the results.
3. Select Apply.

For more details, you can check out the article: Use the audit log in QuickBooks Online.

With regards to your invoice payment concern, are you referring to how QuickBooks records them using a reference number? If so, you can set your own preference number when recording the invoice payment. You can either record them as one transaction or by bulk. This depends on how many invoices are marked as received.

Additionally, there are several financial reports you can run to track your sales income in QuickBooks. They will show you helpful insights on the things you buy and sell, and the status of your inventory. 

If you're reffing to something else, please let me know by commenting down below. I'd be glad to provide further clarifications.