You can use Paypal for getting flat orders and also subscriptions that CAN be included to your affiliate program.

Setup Auto-Return

First of all remember to setup "auto-return" in Paypal.
Here is how:

1. Login to your Paypal account
2. Click on Profile tab.
3. Click the "Website Payment Preferences" link under the Selling Preferences column on the right.
4. Under Auto Return for Website Payments, click the radio button to enable "Auto Return."
5. Insert your server's URL where JVM is installed, example: http://www.yourserver.com
JVM will get the return URL and work with it without the need to define the exact URL of the script.

Flat orders

If you want to get flat sales for a Product through Paypal, then check the "Use Paypal" box and include your Paypal email address.

Subscriptions

Check the "Use Paypal" box and include your Paypal email address.
Check the "Use Paypal Subscriptions" box and fill the rest of the details.The interface for Paypal subscriptions is the same with Paypal's, so if you know how to setup a Paypal subscription you know how to set up JVM too. Otherwise, login to your Paypal account and read about how to set up subscriptions with your account.

Below you can find an example for 3 monthly installments.

Use Paypal
Paypal Merchant Primary e-mail  
Use Paypal Subscriptions
Length of Billing Cycle (for subscriptions)
Billing Cycle Unit (for subscriptions) dayweekmonthyear
Stop Recurring Payments After The Number of (optional)
Re-attempt if subscription fails at first attempt

TRIAL subscriptions

Below you can find an example for a trial subscription of 1 week for $4.99. Once the week is over the customer will be charged for the price you have setup this product until he cancels.

Use Paypal
Paypal Merchant Primary e-mail  
Use Paypal Subscriptions
Length of Billing Cycle (for subscriptions)
Billing Cycle Unit (for subscriptions) dayweekmonthyear
Stop Recurring Payments After The Number of (optional)
Re-attempt if subscription fails at first attempt
Length of Trial Period (leave untouched for no trial)
Trial Period Unit (if any) dayweekmonthyear
Trial Price (leave empty for a free trial)

Make JVManager work with third party's scripts after payment

Notice this field:

Forward IPN to another system
(enter a full URL starting with http://)

By defining a URL in that field you can make JVManager to work with any other script that requires IPN after Paypal.

Here is how it works

Suppose you use Script SS for a separate membership site on another server and that Script SS asks you to add a specific URL in Paypal's IPN field - say this URL:

http://www.serverhere.com/scripthere/script.cgi?functionhere

All you have to do is to insert that URL to JVManager's "Forward IPN to another system" field. JVManager will get the payment through Paypal.com and then REDIRECT PAYPAL'S IPN SYSTEM to the URL defined.

This is a powerful features since it allows you to run various scripts on various sites while using JVManager for getting payments through Paypal.com and without the need to register a new Paypal account for each separate script (for setting up a separate IPN for each script.)