If I am using Fundraising & Paypal, I need to enable IPN.

If I am using Fundraising & Paypal, I need to enable IPN. Will this cause a clash with another site that uses the same Paypal account, but a different email address for payments? Or are they kept separate? The other site is live, and so I am a bit nervous about breaking that by enabling this, but would prefer to have all going to the same Paypal account if possible. Do you know?