All you have to do is present your Pass at the entrance of the museums and monuments you want to visit. The validity of your Pass is calculated from the time of your first visit:
A Paris Museum Pass 2 Days is valid for 48 hours;
A Paris Museum Pass 4 Days is valid for 96 hours;
A Paris Museum Pass 6 Days is valid for 144 hours.
For example: a 2-day Pass activated at 1pm on a Thursday would be valid until 1pm on the Saturday.
No, with the Paris Museum Pass you are limited to one entry for each museum and monument included in the Pass.