I assume you mean enabling the call extension for a Google Adwords Ad? Phone numbers within the ad title/description are no longer allowed in Google Adwords.
You will have no issue using the call extension either with a Google Forwarding number, custom tracking number, or client number. So go ahead.
If you are using tracking numbers, I would set that as the phone number for the call extension and then use the Google Forwarding number option, lowering the time for conversion down to 30 seconds from the default of 60 seconds. This will allow you to get conversion tracking in Adwords for calls as well as send it through to your own tracking number for your own recording purposes.