This is a good question by the OP. I would also refer to re-read of Andy's post above; especially about mfg. recommendations and specifications. They are primarily in the business of making stuff; not in the metrology business.
1. Make a list of some kind of all the instruments involved with the equipment. Typically, pressure gauges don't have serial numbers, so you would want to assign a unique tool number.
2. Determine in the system which gauges are recorded, affect quality, etc. There will be some gauges that need to be calibrated, and some that don't. Make sure (whatever system that you have in-house) that the non-calibrated instruments are not used. Many times I could walk into a facility and talk with the person that operated the equipment. They were quite accurate in knowing which instruments needed to be adjusted. Amazingly, they could tell which instruments were fine, and which ones were way off.
3. The gauges that need to be calibrated can be calibrated in-place or rotated. Saying, you could buy a backup set of instruments for the calibrated instruments and rotate them out whenever you have a calibration cycle coming up. NOTE: If the calibration turn around time is longer than you calibration cycle, you may have to buy an additional set.
4. Calibrate in-place may involve shutting the system down, or like Andy alluded to, having ports where instruments can be verified in-line. I would much rather identify a point where the instrument can be removed and checked across its use range, but hey, you take what you can get.
Now, you may have a system where you have devices that operate another device. For example, you may have a flow switch that turns a pump off if the flow gets too low (where the pump does not burn up). In that instant, I would probably check the flow switch. Other time, a flow switch may turn on a second pump if demand increases; you may decide that does not need to be checked.
Just as a suggestion... it may be worthwhile to bring someone in for at least the first calibration. While I would rely on competent calibration sources primarily, it may be worthwhile to hire a systems integrator that specializes in automating lift stations. They might can recommend for that system what is important, and the best approach to calibrating the instruments.