The game features a fairly complex negotiation system that allows the player to purchase, research, or upgrade new equipment and parts. The OKEs themselves can be upgraded as well through this system, allowing for extended use of the same model for as long as possible. The various companies involved in the negotiation process can also provide valuable information about the purchases of the enemy, allowing the player to better plan for the next advance in enemy technology.

To aid the player in learning the gameplay, Carnage Heart was packaged with an unusually large amount of materials for a console game of the time: in addition to the game disc and above-average length manual, the jewel case contained a 58-page strategy guide and a tutorial disc with a 30-minute, fully voice-guided overview of most aspects of the game due to its complexity.

The main focus of the game is in the design and programming of the OKEs. The OKEs will only be ready to produce once they have a complete hardware and software profile. Both of these profiles are stored in the form of a "card" that can be named as the player likes. It is possible for there to be a total of 28 cards, but in reality the player may use only 25, as there are three pre-made cards that can not be deleted.