I just put in a pool with the PCC2000 IFC System, but your setup sounds somewhat different than mine.
I have a pump solely dedicated to the PCC2000 system, so I don't have to contend with any pressure drop across my filter and don't have to worry about varying pressure drops as filter media get dirty. Before you upgraded, did you have a single pump dedicated to the PCC2000 as well? If you did and if you removed it, you have likely compromised the system. You'll need to ensure that you still have enough water flow for the system to be working. Just because the heads pop up doesn't necessarily mean that you have the correct water pressure at the nozzles. You should probably find a way to characterize the flow to ensure you're not starving it.
Before I put in my system, I contacted the good folks at Paramount to ask some questions. They were very responsive and seemed genuinely happy to make sure I got all my questions answered. You can reach them through their website and ask if your system is still likely to be working per their original design.
As far as the pop-up heads go....none of my floor nozzles stay up constantly when the system is running. Each nozzle is part of a zone that comes on and off per the prescribed schedule. Your system might be designed the same way. Once again, I recommend that you contact Paramount directly with your question. They make a unique design for each pool that has their system installed, so they should be able to pull up their drawings for your pool and tell you how it was designed.
