This is the first question every store asks, so here is the whole answer up front. MTGSL does not sanction events, does not report to Wizards, and does not sit between your store and the WPN. It runs the multi-week leagues and seasons Eventlink was never designed to handle. Your sanctioned play stays exactly where it is.
Eventlink is Wizards' own tool and it is the system of record for sanctioned play. It handles scheduling and running sanctioned events, pairings and result submission through the Magic Companion app, and reporting back to Wizards. Your events appear in the Store and Event Locator. If you are a WPN store, this is not optional and it should not be.
It is good at the thing it was built for: running a single sanctioned event on a single day and reporting it correctly.
Eventlink is built around one event on one day. That model does not stretch, and a store running league play hits the edge of it quickly.
Each event closes out on its own. There is no season that accumulates across eight Thursdays.
Players who arrange their own match for Tuesday because they cannot make Thursday do not fit a same-day pairing model.
Points for a win, points for a kill, points for achievements your store invented. That is what most Commander leagues actually run on.
Three to five player pods, balanced week over week to avoid repeat matchups.
This is not a criticism of Eventlink. Nobody built it to do these things. Which is why almost every store running a Commander league is doing all four in a spreadsheet.
MTGSL is the layer for everything that spans more than one day.
Take an eight-week Commander league ending in a store championship.
Players sign up on your store page. Pods are generated each week and balanced to avoid repeats. Results go in through Discord. Standings update live and players check them themselves. Anyone who cannot make Thursday arranges their match for another night and reports it the same way.
The championship is a sanctioned event, scheduled, paired, and reported in Eventlink exactly as it always would be. The difference is that eight weeks of standings decided who is showing up for it and how much they care.
The two systems never talk to each other, and they do not need to. One is your season. The other is your sanctioned event.
Sanctioned events live or die on attendance, and attendance is a function of whether players have a reason to show up on a specific night.
A season gives them one. Standings that carry across weeks mean a player sitting fourth with three weeks left does not skip. A championship at the end of the season means the sanctioned event that closes it out has eight weeks of build-up behind it rather than a Facebook post on Tuesday.
Run this way, a league is not a distraction from your sanctioned play. It is the thing that fills it.
Want the deeper breakdown of Commander leagues on Eventlink specifically? Read 5 Things Eventlink Can't Do for Your Commander League.
Your sanctioned events stay exactly as they are. Everything that happens between them gets standings, pods, analytics, and a reason for players to come back next week.