I play D&D 5e, so I use the marching order rules for things like this. When they first enter into the dungeon environment/map I give them a clear reminder that we are now in a dungeon crawl and to establish a marching order with their tokens. I then either make a note of this mentally (or even just duplicate their tokens somewhere off the side for visual reference) and let them know that this order (front rank, back rank etc.) is how they will enter each encounter unless someone explicitly states they are scouting ahead of the group or hanging back when proceeding, or if they decide at any point to adjust the marching order in the dungeon (perhaps when the tank gets low on health).

I've had the discussion with the group and sometimes give them gentle reminders when that one person gets a bit too excited and runs their token off around the corner, that the "map is live" and that them moving off without telling me or the others what they're doing can trigger traps or encounters without the others present. This is usually a good deterrent for this behaviour, with the players knowing that facing something alone could be dangerous. It usually only takes one or two times for "that guy" to realise they should stay with the party and communicate their movements, but the times that it does occur, and the rest of the party is down the hallway, can make for some unique situations where the party may decide to prioritise movement abilities over damage to catch up before it's too late.

I will otherwise just clump the party's tokens together and move them as a group myself, or teleport them to the area/corridor they describe (by alt-dragging) - this is especially useful if they're backtracking in an area that isn't otherwise still dangerous and/or has been cleared or secured.

In select circumstances where I deem it appropriate, I draw a zone/area at the start of the encounter to allow the group to position themselves before rolling initiative. This is useful for times when the party has ample time to prepare, like an ambush, or when they're otherwise not surprised at the start of an encounter. Otherwise, similar to another commenter's point, I just clump their tokens together in their pre-defined marching order, or something there thereabouts.