Cooperative molecular communication (MC) is a promising technology for facilitating communication between nanomachines in the Internet of Bio-Nano Things (IoBNT) field. However, the performance of IoBNT is limited by the availability of energy for cooperative MC. This paper presents a novel transmitter design scheme that utilizes molecule movement between reservoirs, creating concentration differences through the consumption of free energy, and encoding information on molecule types. The performance of the transmitter is primarily influenced by energy costs, which directly impact the overall IoBNT system performance. To address this, the paper focuses on optimizing energy allocation in cooperative MC for enhanced transmitter performance. Theoretical analysis is conducted for two transmitters. For scenarios with more than two users, a genetic algorithm is employed in the energy allocation to minimize the total bit error rate (BER). Finally, numerical results show the effectiveness of the proposed energy allocation strategies in the considered cooperative MC system.