Hi,
Reading your description, it seems you make all your payment-management depending on your bank statement only.
Maybe it's necessary to differentiate here. As I'm only guessing on the information you have written and I do not know the details of your processes, it's always the best to get in contact with your local NAV-partner to discuss about an in-depth analysis and training for your particular situation.
Vendor Payments
1) Open Payment journal (nothing to import here)
2) suggest Vendor Payments
3) add/amend manually
4) export payment-file and import into your banking software OR transfer payments manually into your banking software
5) process payments in your banking software
6) wait for confirmation of successful payment and post the Payment Journal in NAV
--> Now your Vendor-accounts are balanced. NAV waits for the confirmation of the payment through the bank statement.
Payment reconciliation (Customer & Vendor)
Details are outlined here: https://docs.microsoft.com/en-us/dynamics-nav-app/receivables-how-reconcile-payments-auto-application
When posting a Customer invoice, NAV automatically expects a payment. Just posting the invoice is enough for this.
For vendor payments, NAV expects to have the vendor payment posted before (see above). This is necessary, to let NAV know when you actually did pay the invoice (for any cash discounts) or if you pay the invoice at all.
The Payment Reconciliation is designed to reconcile the customer invoices, vendor payments and bank ledger entries in one go.
Identifying payments automatically without a corresponding mapping criteria in the transactions (e.g. customer number, invoice number) is impossible for NAV (or any ERP). Therefor any bank charges etc. you have to apply manually. Check this link here for information about the "Text-to-Mapping"-setup: https://docs.microsoft.com/en-us/dynamics-nav-app/receivables-how-map-text-recurring-payments-accounts-auto-reconcilliation
In case bank charges do have always the same description on your statements, you could use this setup to "train" your reconciliation for automatically apply bank charges to your desired account.
For the Payment Reconciliation is one important information necessary to consider: The Payment Reconciliation does work for one bank account at a time only. In case you have different bank accounts for customer and vendor payments, you'll have to import multiple bank statement and process them individually.
Bank reconciliation
This is used in case you work with the Cash Receipt Journal and Payment Journal separately.
Or, use the Bank reconciliation for bank accounts which you use for company related payments (you do not have a customer invoice or vendor invoice). E.g. rent, utilities, interests etc.
Good luck.