I would recommend reading the Help screen before signing an IFA to a MLB contract. It looks like you can offer a MLB contract for 3 years at the 327K minimum like before, but to go past 3 years you must offer at least $5M per year. There are some ifs, ands and buts to this it seems, and no one knows for sure as of yet. If I read it correctly the bonus money may be limited to $10M for an IFA with a $5M+ per year deal. The way it reads looks a little confusing because the bonus money may come out of Player Payroll (like a normal FA) instead of Prospect for this type of contract. That would cut down on money transfers at least. How this actually works I am not sure.
Bonus - Bonuses are guaranteed money that comes out of the player payroll upon signing. Bonuses cannot be transferred through trades or waiver moves. Bonuses are limited to $10 million.
Season - This is the actual season salary that you would like to offer the player. The values in the boxes for the seasons will default to his demands. For minor league contracts, this will be the Rookie league minimum of $7,650. For big league contracts, this will be the 40-Man minimum of $54,000. After a player signs a contract, you must assign him to a team from the Edit Rosters page in the GM's Office. If a prospect is signed to a minor league contract and then assigned to any team but the rookie league, his salary will be increased to the minimum for that level. If a player signs a big league contract for $54,000 and is assigned to the big leagues, his salary will increase to the big league minimum, because this contract type only places the player on the 40-Man roster, not the ML roster. There is a maximum allowable offer of $20 million for any season. The total value of the contract will appear at the bottom of the page. If a you offer a prospect any deal greater than 3 years the minimum annual salary for every year must be at least $5M.