Normally, units occupy only one location while in the realm. However, some oversized units occupy multiple locations simultaneously due to their size, e.g. Mountain Giant. To represent the minion's locations, place the card at the intersection of the sites. When you cast such a minion, declare the area it will occupy when summoned, which must include at least one of your sites, per normal minion casting rules. It may include some of your opponent's sites, but couldn't include the void (without Voidwalk) nor Gnome Hollows (unless its power was low enough). A card's size is determined as it enters the realm (or via other effects, e.g. Megamoeba or The Rack) and becomes one of its characteristics. Therefore, even if a Mountain Giant were disabled or in a Silence aura, it would continue to occupy a 2x2 area. Oversized units occupy each of their locations. Therefore, if grid damage is dealt to multiple such locations, oversized units take damage at each of those locations. For example, a Major Explosion centered on a Mountain Giant would deal 7 + 5 + 5 + 3 = 20 damage to it. An oversized unit could simultaneously occupy both land and water sites, as well as void squares if it had voidwalk. It cannot occupy the surface and subsurface simultaneously, unless it has specific text allowing it, e.g. Megamoeba. When an oversized unit moves, you choose a direction and all parts of it move that direction. If any part of it can't move in the chosen direction, then it can't move in that direction at all. When attacking, oversized units still target only a single enemy unit or site.
When an oversized unit is teleported, it must be to a location or set of locations that are all legal for that unit to occupy, and must not cross regional boundaries unless allowed by card text. If the destination of the teleportation is a single location, the controller of the teleportation effect chooses the position and orientation of the unit, as long as the destination is included in the locations it ends up occupying. For example, Mountain Giant is chosen as the ally for Blink: As the 'nearby location,' I choose X. Now, the Mountain Giant can end up in any of these positions: Since the Mountain Giant is a square shape, its orientation doesn't typically matter, but if it were carrying something, it could also be rotated as desired from the teleportation.
There are many cards that assume units occupy only one location or site. When resolving such effects for oversized units, simply pick a single site or location they occupy. For example, Spin Attack, Leap Attack, and Recall all assume the unit occupies only one location; to resolve them properly, you pick one location the oversized unit occupies.