Whether or not you have administrative access over your Paypal Merchant Account depends on if the relationship is owned between your organization and Paypal, or between Blackbaud and Paypal.  To know if this is the case:

1. Go to Setup>Payment Capabilities
2. Check the User Account field for your Merchant Account
3. If it starts with CNVO, then Blackbaud has the administrative access to this Paypal account

If Blackbaud has administrative access, then you will need to request to have Support look into a specific transaction or to change a setting.  If not, then your organization has the ability to log in directly.