Marked is a new condition that defenders and some soldier monsters can apply to their enemies. By itself, it gives a penalty to your target if it attacks anyone but you, which helps defenders and soldiers fulfill their role on the battle grid. Often, though, there are other effects that serve as riders on the marked condition. For instance the paladin's divine challenge -- that class's signature marking ability -- does some amount of radiant damage once a turn when the target of divine challenge attacks someone other than the paladin who marked him. Of course, the fighter (the other Player's Handbook defender) features a different effect, dissuading her mark from taking the battle elsewhere. Oh, and this is really important to remember -- a creature can be marked by only one opponent at a time and new marks supersede old marks.
So like the combat advantage granted by flanking, marked is relational in nature, but unlike flaking, it can't be apprehended purely by looking at the battle grid. In simple battles with one defender or soldier, you won't have any trouble at all -- just have the defender's player keep track of it -- but when you have two defenders in a group (like I do in my Castle Greyhawk paragon-tier game) or a group of mark-using soldiers in the encounter, keeping track of the condition can be a tad tricky, and you'll probably want to use a rigorous method for tracking the condition throughout the rounds.
The method I've been using lately is marking the bases with magnetic, colored counters called Alea Tools. Each character or monster that can mark in an encounter is given his or her own color, and when a target is marked, that color is placed under the base. Alea Tools also offers a tool to create 1-inch magnetized pads that you can put on the bottom of the base to make sure that when you move the mini, the marker comes with it. Last time I was at my local game store, I also noticed that Gale Force 9 offers a magnetized miniature base kit. You could also use beads, like I do for the bloodied condition.
