Properly applying payments to invoices from external website?

Properly applying payments to invoices from external website?

Hi Folks, 

I merrily thought that having my Stripe Payments enabled with Zoho and fetching payments daily (also accounting for the fees automatically) for my external web store hosted on Big Commerce paid out the invoices in Zoho.  It does not.  It simply balloons my Stripe Clearing account with the Net (after fees revenue) "Sales Without Invoices" entries leaving the invoice unpaid.   Now, this makes sense as I noticed today trying to understand why there were so many overdue invoices...although I did this process based on a Zoho rep recommendation about 6 months ago.

I was amazed today to be told there was no way to apply payments to my manually entered invoices I created in Zoho to mirror those external (non-integrated) website sales. I was told to "disable" the Stripe feed, continue to create invoices in Zoho to account for those external Web sales, then apply manual payments to those Zoho invoices.  I am concerned that by doing this, it will also break the integrated and payment facility for those Zoho retainer invoices or invoices that clients can pay directly through their portal or email from within Zoho using the built-in Zoho link.  

I am unsure as to how to proceed.  If someone knows a way to "pay out" these invoices manually and draw down the Stripe Clearing account net revenue easily and has a work-around... please let me know.  

Otherwise I will disable the Stripe fetching, and payout the invoices manually and then Journal back the Stipre fees to my separate Strip Processing Fee account I have to monitor and account for those fees separately as I do not want them mixed into "Bank fees".

Cheers, Bruce