ISO14644-1 is the room certification; it is performed as per the exact standard issued. The first step for pharmaceutical customers is to certify the cleanroom to ISO standards. Once performed they now move to step 2 - cleanroom monitoring.
The big difference between the two is that room certification follows a formula and is used to calibrate the HVAC system. Monitoring is a risk based approach used to prove continued compliance of the room. The only point at which these two exercises ever meet is that in having an installed system the frequency of re-certification can be extended to 24 months (ISO14644-2).
You cannot certify a cleanroom using a monitoring system, only extend the interval between re-certifications. The sample points are in the wrong place etc.
For information on how to choose a particle counter read Selecting Airborne-Particle Counters for ISO Certification of Cleanrooms.