Apologies if you find this post a bit too long to read. I've proof read this thing over and over and hopefully it won't need much editing beyond what I've already done before hitting the submit button. One last thing, if you're struggling with your game and looking for guidance from an experienced player then I'd recommend visiting the Society of the Cooks thread Calling all cooks - Society of the Cooks Forum is now open.
Glossary
Drop: Your starting territory or territories upon game initialisation.
Control Bonus: Bonus troops gained when occupying the same colour/type/group of territories, or when the special conditions are met for occupying certain territories(varies between maps, is usually indicated on the map legend).
Territory Bonus: Bonus troops gained after the default 3 per turn when you conquer and hold 12 or more territories, +1 extra and an additional +1 for every three territories after 12 that you own.
Stack: Usually refers to large numbers of troops located in one territory.
The Topic
Territory Bonus Vs. Control Bonus
More territories or bigger stacks?
One of the real 'quality versus quantity' dilemmas when playing on a new map. I'm often wondering if I should go for the Territory Bonus or the Control Bonus, more often than not it depends on your drop. There are a shed load of maps to choose from and sometimes it's just not easy to decide what territory to go for(if any). It all rather seems to be a load of swings and round-abouts, but we'll try and make sense of this muddle, first off we'll start with the pros and cons of the Territory Bonus and the Control Bonus. The Territory Bonus yields low rewards to start with, but once you start accruing additional territories the rewards rack up. Losing a territory or two has little or no impact and will likely only knock off +1 from your extra troops bonus. So hard to gain and hard to lose, with low but consistent reward increments and low maintenance requiring only a very few troops to occupy your territories. On the other hand the Control Bonus yields a reward that is dependent upon the number of territories of the same colour/type/group that you're trying to control. It is also a rather all-or-nothing affair(depending on the map) where your bonus can be broken if just one of the territories you require control of is wrested from your ownership. Can be difficult to gain and sometimes easily lost again, but yields rewards directly proportionate to the difficulty of holding all the required territories, may require a few stacks to ward off attackers until your next turn.Now lets talk through some of the factors that will influence whether you plumb for a Control Bonus or a Territory Bonus.
1) Drop
2) Map size
3) Number of players
4) Spoils
1) Drop
This will have the largest impact on your initial decision making, if you drop mostly on one colour/type/group of territories then it's that much easier to claim the remainder that lie outside your control and reap the Control Bonus it affords. If you have a difficult drop with no two territories under your control adjacent to each other, then you'll probably want to go for the Territory Bonus instead. Try to go for the cheap shots like territories with only one troop occupying them if possible. If you are playing on a map where you start with just one or two territories on your first turn then it'll be more profitable to go for the Control Bonus.
2) Map size
The larger the map, the more territories you will start with on your first turn, generally speaking. On tiny maps like Doodle Earth(total available territories is 18) it's clearly best to go for the Control Bonus, as trying for the Territory Bonus will be difficult to say the least and just make you a magnet for attack from all the other players. On huge maps like Conquerman(total available territories is 141!
) it's a lot easier to gain and hold the Territory Bonus, which starts at 12 territories owned and gets higher with every additional 3 territories. The Control Bonus is still useful, but not nearly so critical to success on a large map.3) Number of Players
Always second to map size the number of players in the game will affect how many territories you start with in addition to how big the map is, more players means fewer territories at the start(if starting with more than one territory in the first place). So basically the same considerations as map size, what you do depends on how many territories you have at the start. Of course with each additional player comes a potential additional attacker, should someone successfully galvanise the collective to attack you on the premise that "you're getting too strong".
4) Spoils
A no spoils game will keep things nice and simple, it's just you, your opponents, and the dice. In a flat rate spoils game you'll get an occasional boost of extra troops when you cash in a set, the Territory Bonus and/or Control Bonus are still important. But your ability to retain any bonuses can change quickly when you or your opponents cash in sets, contingency planning is essential if you're to retain your hard won bonus!
In an escalating spoils game, the Territory Bonus and Control Bonus will quickly become irrelevant from about round 7 and onwards(especially in games with 5 or more player). If you've managed to bag a bonus or two, don't try to hold on to them too hard once players are getting 20+ troops per set of cards, you'll just be drawing attention to yourself. 
Summary
I think that covers everything for now, I'll incorporate useful information from posts by other users, especially if it's something I've missed. I'll take the opportunity once again to recommend to new players a visit to the Society of the Cooks thread Calling all cooks - Society of the Cooks Forum is now open. You don't have to be a Cook, but it helps!
