alchemical ammunition is made as a single bullet
there is afaik no official ruling as of yet for how singular bullets interact with magazines
also note that many alchemical and magical ammunition has an action to activate it which makes it with a firearm (or another reload weapon) that you need one action to load and one to activate (which makes them a action inefficient choice anyway)
thinking logicly (which I know not always applies) weapons with a magazine probably have no point to really enter special ammunition, so that would mean going ahead and out of combat removing a regular shot and then filling it with the special ammunition in question, which would make the loading of the ammo just part of loading the magazine, but of course comes with the disadvantage of having less flexibility in its use
You definitely don't create magazines when creating alchemical or magical ammunition, you create single bullets/arrows/bolts/sling stones/etc, as Tactical Drongo explained.
Ruleswise, there is no "reloading" a magazine for a repeating weapon. The ammunition is the magazine, as the tables show. Realistically though you should be able to put pellets in an air repeater magazine, bolts in a repeating crossbow magazine, etc.
That's something you'd need to talk to your GM about tough, because it requires a lot more bookkeeping on your part as a player. Not only would you need to keep track of which magazine is loaded with what alchemical/magical ammunition, but in what order too. Plus if you fill up a whole magazine with ammo that requires activation, you're basically giving up one of the main advantages of repeating weapons, since you'd need to activate ammo after every shot or you'd waste it. Which is effectively like reloading after every shot.
When I played through Guns and Gears our GM compromised with the Gunslinger and allowed them to single-load alchemical/magical ammo into their Repeating weapons, just to save everyone a headache.