Trying to untangle the reading order for 'San Chan Kun' is a rite of passage for fans because it wasn't published in a straightforward way. The original serialized web novel is the core, but it's massive and still ongoing in some spaces. Most people I know started with the published light novel volumes, which are a more polished version of that early web content. Those are numbered, so just follow Volume 1, 2, 3, etc.
Now, the tricky part is the side stories and alternate universe stuff. There's a whole series of side stories focusing on other characters that pop up chronologically around Volume 4 or 5 of the main story. You can read them as they were released, which is what I did, but it honestly breaks the flow. My advice? Read the main light novel sequence first, straight through. Then, circle back for the side stories as a bonus treat. They're fun, but they don't advance the primary plot.
I've seen some forums suggest mixing them in, but unless you're a die-hard completionist, it's not worth the mental juggling. The main narrative is plenty engaging on its own.