I ran a transaction and it said accepted but so far it does not show up in my PayPal Pro/Virtual account.

Are you sure you are not in Test Mode? Click the config screen and make sure Test Mode is OFF. PayPal may delay your first payments for several days after you first sign up. You may contact vt@paypal.com for help.

I ran a transaction and it said accepted but so far it does not show up in my Authorize.net/Cybersource account.

It usually takes 2-3 days for your funds to appear in your bank account in the case of Authorize.Net or Cybersource. You can always verify that transactions are indeed going through by logging into your control panel and searching for "Settled Transactions". If you've waited at least 3 days and nothing has shown up, please check the following:

1. Make sure both Swipe and Authorize.Net/Cybersource are not in Test Mode. 
2. Contact your merchant account provider (Applied Merchant?) for investigation. Sometimes your funds may be held if something was incorrect in your application. They can usually release this hold after talking with you
3. If your account is with PayPal, funds usually appear in your account immediately. If they are not showing up, please confirm your account with them is not in test mode, that your account has been "approved", and contact them to resolve any issues with your account.