1) Right click Steam icon in desk tray, pick SteamVR. Wait until you see it started up.
2) Power on BOTH controllers. Wait until they both have green lights.
3) Power through all your trackers one by one waiting for the next one until the previous units light is green.
At this point, if you have assigned your trackers all correctly in SteamVR all apps should work correctly.
If you desire to change to a second set of controllers during a sessions of VR, SteamVR does NOT allow for this procedure currently in it's native configuration. You'll need to shut down SteamVR , and then follow the instructions above, but with the new set of controllers.
On the other hand, pucks/trackers can be powered off and replaced mid stream by:
1) Is the tracker currently powered or has it run out of battery already?
a) POWERED: Cover the tracker / hide it from lighthouse view, and watch the SteamVR panel, the one that turns grey is that tracker. Right click it and pick turn off.
b) NO POWER: Skip this step.
2) Turn on the new tracker wait for green light.
3) Go into Tracker Assignment and assign the new (green icon) tracker to the position you replaced (knee/foot/whatever)