If your 29er gets a flat and all you have a is a 26″ tube go ahead and use it! Check this out.
The trick is to hold down one side of your wheel while you work in the tire onto the rim. Make sure the tube is deflated while you’re doing this, it makes it easier to mount. After you have it mounted, you’re ready to air it up and get back on the trail. I own a handful of 26er and 29er bikes, and all I buy are 26″ tubes because they’ll work for both.