This can be set in your E-junkie payment preferences, but until we finish with our non-flash interface the way to do it is a bit tricky:
1 - Go to Seller Admin > Edit Payment Preferences
2 - Check the "Enable Authorize.net" box. Note that this will disable your Website Payments Pro option, but do not worry about that.
3 - When the Authorize.net box is checked you get a list of which credit cards you will accept. Just uncheck the boxes for Amex and Discover
4 - Check the "PayPal Website Payments Pro" box at the bottom again and submit your changes.
Once we finish upgrading the admin interface the means to do this will be available for both Authorize.net and PayPal Pro but the settings will still stick even though they do not show with the PayPal box selected. Your checkout page will not list Amex and Discover as options.