As there is no details furnished with regard to water system and in which lab the answer could be generic
Q. It is necessary to make the qualification of design and installation?
A. Yes, As a good laboratory practice, IQ/OQ should be performed by the manufacturer upon request by the user.
Q. The company has standardized sanitation and cleaning procedures for the equipment and established times to change spare parts. Are phases 1 and 2 modified in any way since I can not change them?
A. No, should adhere to manufacturers time, as they might have validated.
Q. If the equipment is supposedly qualified by the company, should it only monitor the points where the water is taken?
A. There are two ways to address it, as the lab water equipment is qualified we need to look at the validity of the sensors. Till the validity time you can monitor the quality delivered at the point of use, Meanwhile get ready to verify the sensors in a periodic way (once a year?? As per the lab criticality) to avoid any surprises.