If you go with S2Member, you would probably just use the PayPal button code they provide, and that would simply bypass E-junkie entirely, without interfering with any other products you might be selling through E-junkie.
As for Wishlist Member, since we don't provide that software, we can't provide support for it, nor are we even familiar with it, but if you could describe in detail what role you'd need E-junkie to play with that solution, we could explain if and how that might be possible. For instance, if it depends on receiving PayPal IPN to confirm payment, you might be able to have our custom/3rd-party Integration forward the order details to their IPN script after we receive the original IPN from PayPal:
http://www.e-junkie.com/ej/help.integration.htm
If you'd like some more direct assistance setting this up, we can recommend the competent, E-junkie-experienced developers listed in our directory here:
http://www.e-junkie.com/ej/developer-directory.htm