If you have the system set up correctly, the pump should be running whenever there is a call for heat. If it is operated by a separate aquastat that cuts out at low temp, that aquastat needs to be adjusted down to a few degrees below the programmed low setpoint of the Intellicon, to guarantee that it always purges the boiler heat down a temp where it kicks the burner on when there is a call for heat.
Since the boiler is natural gas you can safely program the low point of the Intellicon to about 130F, but if oil-fired it can be set it no lower than 140F, even if the flue has a stainless liner. Even though you won't get significant condensation on the heat exchanger plates by setting it 5F lower than that, the risk of flue condensation dripping back into the boiler rises. The default setting of 145F is safe for even the worst-case oil boilers hooked up to terra-cotta lined flues, and even most of those would be fine with a 140F low-temp.
See page 6 of the manual regarding boiler-bypass and return water temps. The manufacturer recommends 140F as the low-limit for return water temps, which is fairly conservative, probably TOO conservative. With an atmospheric-drafted gas boiler like you can probably take it all the way down to 125F at your altitude. At sea level even with optimal mixtures it's hard to get much condensation at 125F boiler temps even with boilers designed to make use of that condensation. The lower atmospheric pressure at 5K' makes it harder still, just don't crank it down to 120F. But if you want to play it safe, set the low limit on the Intellicon for 130F, and time how long it takes to get back up to 140F, which SHOULD be pretty fast, several 10s of second. If there is bypass plumbing that can be tweaked to feed a bit more boiler output into the return water mix, set it up such that no later than 90 seconds into a burn the return water is above 130F. (It's fine if it takes longer than that on cold-starts.) If there is no bypass plumbing and the system is running 120F return water all or most of the duration of the burns, you'll have to start bumping up the low-limit.
The lower you set the low limit, the lower the standby losses will be, and the shortest burn cycles will become longer, and more efficiently the system operates. But setting it up to always run at condensing temperatures WILL destroy this boiler in one heating season, since it isn't designed to tolerate condensation on the heat exchanger plates.