I've been shooting Krags for 50 years now and have yet to have needed to bed one. That said, if I were to bed a Krag I would do pretty much what Dillonbuck just said. Since the Krag has no recoil lug
per se, there's not much you can do up around the receiver ring except give it a good bed to rest in, along with the first couple inches of the barrel. The two action screws are both at the back of the receiver (for you non-Krag guys), so most of your work will be back there as well as bedding the back of the wall of the magazine box (which is in effect your recoil lug). Bedding that area will almost automatically include the front action screw. I would relieve the inletting around the rear action screw boss for epoxy bedding (it goes pretty deep into the wood so there isn't much need for a pillar there), at the same time create a pad of epoxy under the length of the tang. Definitely maintain a clearance cut behind the tang as you would with any bolt gun- I like to do a 1/32" undercut leaving the top surface of wood fairly tight to the tang, it gives a little room for compression while creating the illusion of tight inletting.
Applying a skin coat under the magazine box wouldn't hurt. Anything you can do to strengthen that thin piece of wood there would be beneficial. Definitely one of the Krag's weak points.
Probably more important than bedding though is how well the front of the gun is anchored in the stock. Since the two screws are way in the back, it relies a lot on the barrel band to keep things from trying to pivot up and out of the stock upon discharge. That band (or front barrel screw in the case of a sporter) has to be tight to the barrel or you'll get erratic accuracy and stock splitting in the back. To that end you probably ought to bed the barrel too, in a patch under where the band is.
Hope this helps. Honestly though, if the thing is well bedded in the wood as it exists now, and the band is tight, I would concentrate more on load experimenting than fretting about bedding the thing. The barrels along with bore condition, groove diameter, and throat diameter are what really drive a Krag's performance. Every Krag I ever owned, in arsenal stocks and with a decent barrel, would group 1½-2" with issue sights at 100 yards (when I was young and could still see them), and a fair bit better with aperture rear sights. My most recent Krag custom job (new Criterion barrel, Lyman 48 sight, among other things) will do 1" often enough that I'm tempted to call it a MOA gun- as long as the light is good and I'm not hungover.