Fundraising Plug-In and PayPal (multiple portals and IPN use)

I am currently using my existing PayPal account on my main website to process general donations to our non-profit. When donations are made, we receive basic email notifications. Now I have added Fundraising to a subdomain for specific projects and will want to use my same PayPal account to receive project donations. We are NOT using IPN for our main donation portals. So — if I set up IPN for the Fundraising plug-in, will it have any unexpected or negative effects on my PayPal account. I assume not, but I want to be sure about it.