Hi,
No, there is no option in Integration Manager or eConnect to import AP payment applications.
To address this need, I have developed a product that can import AP Manual Payments and apply them to open AP invoices. It allows you to specify a payment file, and a separate application file, and can perform the manual payment import & apply in a single step, or separately if you wish.
http://dynamicsgpland.blogspot.com/2013/07/ap-payment-application-import-for.html
If you have any questions or are interested in a trial, you can contact me at:
precipioservices.com/contact-us
Thanks,
Steve Endow
Precipio Services
Dynamics GP Certified Trainer
Dynamics GP Certified IT Professional