There are three ways to deal with extra troops, which you may have either bought with gems, recruited, or had awarded to you by your league's tournament activities.
1.) Use them. If the player has 2M it may be because they are preparing for battle
2.) Feed them. Some people log in several times a day to farm for their troops, or to send food from another realm where they do NOT have 2M stationed.
3.) Starve them. Sometimes a player received bonus troops while they are offline, and when the food runs out, they starve. Other times, the game sends food along with the troops, and if the alliance remains active in the tournaments, this could maintain an high troop population for quite a while.
@Teighernach (US1) Upgrading is a permanent improvement. If you upgrade your macemen, for example, to level 5, then every maceman you recruit from now on will be a level 5, in all kingdoms.
Bonus troops refers to the ones you are awarded from tournament play, daily log-in rewards, leveling up, etc.