More money in Franchise mode during free agency or season:
Complete your first season in franchise. Begin the next season and notice there should be some great free agents that can be acquired (for example, Cliff Lee, Big Papi, Torii Hunter, etc.). However when you try to sign one, you may not have enough funds. To bypass this, go to "Manage Roster", select a player, and go to "Edit Player". Scroll until you find "Contract". This will show their current contract (for example, $1.4 million and 4 years) and each year's salary. It also gives you the option to decrease or add a year, or even drop his salary very low in the final year, etc. For example, as the Cubs select Lee. Max his contract out to ten years, and set it to the lowest amount on each year ($300,000). Save the game and go back to free agency. Sign Torii Hunter and you should notice that you have more money available. You can do this to as many players as desired.
Never lose player on your team to free agency:
Go to your "Mange Roster" menu and edit a player (for example, Carlos Zambrano). Scroll to his contract and you will see the amount of money and years he has remaining. You can lower the amount of money and add as many years as desired. You will never lose him until he retires.