The first direct-vent unit I ever did, I did almost the exact way, except I only used the flue for the exhaust.
Well, the installation looked very clean and neat, except the unit would never start. I was sure it had to do with a defective unit, but the first question the tech guy asked was how the intake and exhaust pipes were run. Because the units are so tightly sealed, and are designed to go in similarly airtight homes, any leaks can be extremely hazardous. Therefore, the units come with a myriad of sensors, and if everything is not just right, the unit wonít light.
What was happening in my case was the pressure of the cold air coming down the flue was enough to set off a sensor. At least, that what what they thought. These units could only tolerate about a 5í rise in the pipes, but the horizontal run could be 30í. They (the pipes) also needed to be located next to each other, with the exhaust receiving a 90-degree upturn outside the house, and the intake, a 90-degree downturn. The exhaust also required about a 6Ē vertical piece of pipe. If you go to a new home development that uses high-efficiency heaters, you can easily see what I am talking about.
I am not sure, but I believe the reason the 2 pipes need to be next to each other has something to do with the sensors as well. If you were to run one pipe to one side of the house, and the other somewhere else, changes in wind and pressure in one place may cause the unit to ďdetectĒ an imbalance, and shut down.
Essentially, the units are designed to vent out the side of the house, and usually this is accomplished by running the pipes between 2 floor joists, and drilling 2 holes through the end plate. If this unit were going in your basement, the 2 pipes would run between 2 first floor joists, exiting on the side of the house just below the level of the first floor. Pick a spot that is not getting in the way of any obstacles, like a deck or whatever. Personally, that would be far less work than trying to use the existing flue, anyway.
Feel free to post other questions on your project.