I used to haul equipment for a living. There is alot of flexibility on chaining things down, and everybody does it differently, but a couple basic principles.
On a small tractor, (mine) I put a clevis through the draw bar hole, and run a chain through that, and run another chain through (around) the front bumper assembly. The rear chain pulls rearward, and the front chain pulls forward. You don't really want the chains pulling down vertically, as this can allow some forward or backward movement. On the rear, you could also go around the axle shafts with 2 separate nylon straps. That's another option.
If you have a loader, put it all the way down. Not really necessary to chain that too. It won't go anywhere, but you can if you want. Won't hurt.
Also, if my backhoe is attached, (there may be some disagreement here, but this is my feeling) I lay the boom down on the deck so the extra weight is not being carried by the tractor. Then I chain that to the deck too. A 1000LB backhoe bouncing down the road at highway speed can't be good for a small tractor, or the pivot pins for that matter.
One thing you Never want to do is use hydraulic pressure to secure a load. For example, don't throw a chain over the loader, and the 3point hitch, and lift up on them to take up the slack and tighten the chain. The hydraulics will leak down, and the chains will be loose where you get where you're going.
Lastly, try not to overtighten the chain binders. Tightening them draws the tractor down, and literally adds hundreds of pounds of weight to your axles and tires. Don't go crazy. And stop to check your chains periodically on long trips.