If you use an outboard phase-cancelling noise eliminator (such as MFJ-1026), that would also be placed in the coax between the radio and antenna. If an amp is used it would be placed between the amp and antenna. It doesn't really matter if the noise cancelling box is before or after the SWR meter.....
A word of caution.....most of those type of devices are rated at 100 watts max throughput, so if you run a big amp, using one is pretty much out of the question.
I have a nice Daiwa SWR meter, but I don't keep it in-line. I use it after I make any major changes to my antennas, and after that I unhook it and put it away. My antenna tuner has a decent built in SWR/power meter and under normal daily operating conditions that is what I rely on.
My number one setup is a Kenwood TS140S straight into a Kenwood antenna tuner/antenna switcher and then to one of two antennas.
Number two setup has a Cobra 148GTL into a A/B biased Palomar 200 and then into the same Kenwood antenna tuner/switcher from there. I'm a big believer in having as little as possible in between the radio and antenna !