I have had some success staying in the black with Dorchester through (only 1/2 way through first season on FM 2013 but these seem to be working as well as they did in fm 2012):
1. Staying below wage budget, use loan and non-contract players as much as possible.
2. Getting a parent club if you don't have one. Helps with annual fee, loan players and a home exhibition game against larger rep team.
3. Exhibition games against bigger teams in pre-season and during any lulls during regular season. Away if that maximizes your take, Home if the expected profit is bigger than the away option. Because of game day expenses, I usually take the Away option unless the best Home game is expected to be at least 10% more profitable than the away fee.
4. I set high cup bonus in the lower leagues as cup runs can be very profitable and the "high" bonus seems really quite small relative to take in the lower divisions. Never formally done the maths, so I may be off on this, but it suyre seems to be the case.
5. Activate any and all buyouts that the board negotiates. The money is almost always worth more to me in hand than some potentially larger future payment is in the future.