If you use journal entries to pay the invoice the invoice will never show as being paid, you must make the payment using the receipts module or the payment will not be linked to the invoice.  You should test this on a test copy of your database to confirm!  You may have to set up one of the temporary accounts for stripe to allow the funds to show as a bank for it to be available in the payment module.  I am not an accountant so I may not be using the correct terminology!

Based on your message subject, I would say that you likely have the correct sequence (see assumptions below).  What Ginkgo Bike is indicating is also correct but only if you are using Sage 50 for posting invoices in the Sales/Receivables module and he is referring specifically only to General Journal entries.  His advice is good about testing on a copy of your file as long as you can import the information from Stripe multiple times.  Always back up your file before you import from a third-party product.

My assumptions are what you indicated in your subject message.  Invoicing and receiving funds is done through the Stripe program and both are posted directly to the Sage 50 Canadian program through General Journal Entries.  I am not assuming that invoicing is done in Sage 50 and the receiving of money is done through Stripe and posted directly to the company file.

I took a quick look at the Stripe website because most companies ignore Sage 50 Canadian in their integrations but apparently they have a good developer program.  I am assuming you are doing the posting through that method and that you are properly posting to the correct modules.

Lastly, I assume you ignored sales tax for simplicity but if not, your original journal entry should have included sales tax if it is applicable on your sales.

Hi.  Thanks for your response.  I do realize that I would have to use the A/R module however knowing what is going on in the back ground of the system is important.  My goal is to make sure I have an accurate A/R account along with an accurate account that shows what is still outstanding from Stripe.  As far as I can tell I am not able to import from Stripe multiple times.  The import is done automatically when I open Sage. 

The invoicing is done through Sage.  Once the invoice is emailed to the customer they will see a pay now button which will take them to Stripe for the payment.  Once the payment is complete Stripe holds the money for a few days then does a weekly deposit into our account.  Because everything is done automatically I am a bit nervous.   I think I will give Stripe a call and see what they say.  I dont want the first payment to go through and cause a big mess in my system.  If they are able to resolve my concerns I will post it here.  Also you are correct about me ignoring sales tax for simplicity.  :)  

Hi.  Thanks for your response.  Thank you for the idea of the test database.  I will see if I can figure out how to make that work.  I do realize this all goes through the A/R module.  My concern is more on how it goes through the module and what accounts are effected.  

Unfortunately, I have no direct access to the systems you are setting up and have never used them (none of my clients do). However, the marketing materials on the website indicates seamless integration with Stripe and PayPal.  Therefore I would expect the proper journal entries for payments into the A/R system.

I would make sure I know what payments have happened according to the Stripe reporting, then open Sage 50 and see if those entries post payments against the invoices applicable.  Then follow the journal entries to see if they show up as you expect.