You should decide whether you want to enter Germany using your Canadian or US passport. Based on what you've told us, there is no reason to prefer one over the other, since US and Canadian citizens have the same privileges of visa-free entry into the Schengen area.
Absent any other reason to prefer one passport over the other, you should just pick the one that makes your life easiest. For example, if you can use one passport for the entire journey, do that, so you don't have to worry about switching passports while you're traveling.
This will largely depend on where you're traveling from to reach Germany, and where you're traveling to after you leave. If your trip is a round trip from the US, use your US passport. If it's a round trip from Canada, use your Canadian passport. If it's a round trip from any other country, use the passport that you used to enter that country.
If you are planning to use only one passport, should you take the other one? This is a matter of debate. It's useful to have a spare, as noted in pnuts's comment, but more to the point, you may find yourself in a position where you need the other passport and don't have it.
For example, if you're traveling with your Canadian passport when an emergency arises requiring you to travel unexpectedly to the United States, you would be in a difficult position if your US passport were still in Canada. On the other hand, if you don't have your second passport with you, you're perhaps less likely to lose it.
I prefer flexibility, so I generally bring both of my passports with me whenever I travel internationally, but others disagree.