How to separate landing page and pop up form flow emails (both have different type of discount)

@Rossana 

First you can connect the 2 different opt in methods to 2 different lists, that would probably be the simplest way.

Other way is to separate them with the custom property source. Depending on how they subscribed to your account they will have different source property. One should be the pop up form name and the other one not sure how people subscribe to your landing page but anyway it won’t be the pop up form source. 

So in your current setup with 2 different flows triggered by same list you can add flow filter property source equals “sign up form” (this will be called different depending on how you named the source for your sign up form) and then on the other flow for landing page say property source doesn’t equal that same property about the form.