How best to terminate two high efficiency systems
Are you sure you have a high-efficiency water heater? If you didn't pay about $1500 or more for the unit itself, you have a low-efficiency water heater, and the distinction is important because you can only use plastic pipe for the exhaust ducting with high-efficiency condensing gas-burning equipment. Anything less than 90% efficiency needs metal exhaust ducting. and special clearances to combustible materials (like plastic pipe) due to the high pipe wall temperature.

Your level of confusion as well as the dangerous nature of what you are asking about leads me to worry that there is a nonzero chance that you will blow yourself up or set fire to your house. If you insist on continuing the work, I would recommend that you read the gas plumbing and venting code in your municipality and follow the guidelines set forth there.

If you choose not to do this and continue with this as a DIY job, please understand the risks to life, limb, and financial livelihood posed by unsafe gas work.