Air Carrier First Officer reports maneuvering around build ups during the arrival with the autopilot disengaged. LNAV/VNAV are engaged when complete but the autopilot is not; resulting in an altitude deviation.

Narrative

Aircraft descended to 11;400 when cleared to 12;000 in vicinity of RPTOR intersection. During very busy arrival into ATL; after descent had begun; a different arrival than what had been already programmed was given. The new clearance was for HERKO arrival; cross HERKO at 12;000 . We were faced with buildups to over 20k in front of us just prior to HERKO and asked for a deviation to the right. While Captain was busy reprogramming FMC; I disconnected A/P to smoothly deviate over and around buildups. Deviation with several turns made; then direct RPTOR. Hand flew to 12;000 and reengaged LNAV/VNAV but did not confirm Auto Pilot re-engagement. Noticed that aircraft was not turning after RPTOR and while I took control to turn aircraft. I did not maintain proper altitude. Captain and jumpseater both noticed and advised lack of A/P engagement. I should have received acknowledgment when I disconnected the Auto Pilot. Failure to do so and to not verify proper Mode Control annunciation caused me to deviate from assigned altitude.