Best way to update primavera schedule, based on physical % complete from site

Hi Guys, 

Please provide me with your opinions for the problem stated below.

I have a baseline schedule which is resource loaded, but not cost loaded.

The "% complete type" adopted is "duration % complete" . 

My primavera schedule is detailed till activity level only, further under activity level - 'objects' and then next level 'opertions' are tracked separately in another in house software.

Update is done at operations level on inhouse software (similar to steps in P6) based on input from site, and i get a roll up to activity level based on objects (quantity basics weighted).

My concern is the value i get from inhouse software is basically 'physical%complete', my P6 schedule is duration%complete.

So what is the best way to integrate these.