The positive connections should always be battery to battery.
The negative connections need not be, since a good ground flows directly into the ground post anyway.
The positive connections are always made first.
The reason they don't recommend negative to negative on the battery posts is because when the fourth and final connection is made, there is almost always a spark, and if that spark is too close to a battery, it can cause an explosion of any hydrogen gas that may have built up in the battery.
It is possible to damage the alternator or charging circuit of a running car if you screw up and cross connect the jumper cables, positive to negative. For this reason, they recommend that the car doing the jumping shouldn't be running during the process.
Now having said all that, I've jumped numerous cars over the years with my car running, and never had a problem. I always insisted on doing the hook up myself, and never let the driver I was helping do the hook up. I also used to go directly to the negative posts, again without a problem. I stopped doing THAT when I finally understood the danger of a battery explosion. And also because it became a lot harder to make good connections directly to those damned side terminal batteries.
Regards
John
PS: If you HAVE a side terminal battery in your vehicle, there are adapters that can be fitted to them to make it easier to jump them.