The default analog settings on ALTGX transceivers will be the same as you set them to be in ALTGX MegaWizard™. You can set the analog controls in ALTGX MegaWizard "RX Analog" and "TX Analog" tabs (under "1 Parameter Settings" tab). Whatever analog settings you choose during MIF creation will be the applied settings. If you like them to be the same, make sure to set them the same in both MegaWizard files.
You can also use analog dynamic reconfiguration to change analog settings later, as explained in device handbooks or their associated Application Notes.