Captain reported receiving a low altitude alert from ATC on approach to CYYJ; citing differences between the airplane's autoflight systems and the simulator used in training as contributing factors.

Narrative

To start with neither of us (pilots) had been flying this make and model very much in the last few months (though we both had been to sim training recently. Also; my last few legs had been short legs and one had had some weather concerns; including holding; waiting for a thunderstorm to pass the airport; and then needing to land with a tailwind.The morning of the trip; we knew it was a short leg to CYYJ so we set up the FMS and actually got the arrival ATIS before departure. We were doing well with the flight but very busy. We received a clearance direct to DAXET to cross it at or above 4;000' (I believe was the crossing altitude); crossing DAXET we were cleared for the approach. We were just approaching Top of Descent (TOD) and had VNAV engaged so I set 4;000' in the Altitude Selector; then confirmed on the chart the Final Approach intercept altitude of 2;100'. I set 2;100' and told the PF that I was setting it. Approaching DAXET; the PF queried if we were cleared for the approach. I said we were and got confirmation from ATC. After discussing the event later; I missed the fact that he had turned off VNAV to increase his descent rate. We had the airport in sight the entire time from our clearance to landing. About halfway between DAXET and AGBAR; I started to get caught up with my tasks setting up the aircraft and I had an uneasy feeling we were a little low. Before I had a chance to figure out our exact situation ATC told us we were low (about 2;500' MSL) and that we needed to climb back to 3;100' (Min altitude for the segment of the approach). He then issued an official Low Altitude Alert. We told him we had the airport in sight and received a visual approach clearance. We then flew into the airport and landing with no incident. Another contributing factor is the differences between our aircraft and the simulator. This means that every time in training; we have to re-learn the specifics for RNAV approaches for an older FMS; then remember the correct setup for our FMS when using LPV approaches. They are similar; but different and this creates confusion in the way that VNAV; APP; and LNAV modes should be used between the sim and the aircraft. Having both been to sim training recently and not flown the aircraft much afterwards; we both were not as familiar with specific modes and FMS/FD setup as we sometimes are.In the future; I'd make sure to clarify better with the PF when I set an altitude below the current restriction. Also; since it was his first leg as PF on the sequence; I'd do a better job monitoring an PF actions on busy short legs. Lastly; I'd continue to do a thorough setup of the aircraft like we did before the departure to make sure we were not further behind the aircraft than we were at the time.