Paul,
Your 2nd question update leads me to ask what Dynamics Service is running? If I was sending EFT files via a Bank Service then I am wondering are you using AMC Banking? This will send the EFT file via their service to the linked Bank. If I am doing this all manually, then the process is:
1. Payment Journal create list of EFT payments
2. Export EFT File, which generates remittance advices to vendor
3. Generate EFT File to then upload to your Bank. NOTE: In your version of NAV 2018, the Generate EFT File will open a Save As window which the user specifies the location to save the file too. NOTE: The User and NAV must be able to Save a file to that location. So if the NAV Server cannot save a file there, you will get the error. I would have IT map a drive to the location you are saving too.
Hope this helps.
Thanks,
Steve