I use one of these:
You connect it to the city water. I have a little sears air compressor for tires, I connect the end onto the plug and open each valve 1 after the other.
But, don't have all valves close at once, let the air flow from at least 1 valve at all times.
And no more than 40 PSI.
And yes, a bypass valve and hose for the hole house filter.
Where do you have your whole house filter mounted at?