I agree with Dad10's approach, but will add a few thoughts.
First of all, you should not fall into the habit of always batting them as a tandem, or always batting them at the bottom. They will catch on to this. They already know they are struggling. They will swirl further downward at anything they can construe as "coach doesn't like me" or "coach doesn't have faith in me", etc. Even if you are the world's greatest and most positive youth coach, a kid facing failure and humiliation is already in a negative mind set and looking for reinforcement of that self image.
My two cents on how to break the cycle:
Try bunting them. This gives them an opportunity to help the team even while making an out. You should already be teaching the team about a team approach to hitting, with examples including getting a fly ball with a man on third and less than two outs; putting the ball on the ground to the right side to make sure the runner advances while also trying for a hit; etc. If you teach your team that a productive out deserves a round of "high fives" when they come back to the dugout -- and after all, it truly does -- then you can simply bunt these kids a bit and get them into a more positive mode.
The added benefit is that since you have a 9u team on your hands, half the time they'll get a hit if they get the bunt down, or better yet the other team will throw the ball away. Next thing you know your struggling kids are taking the extra base and coming around to score some runs. Since confidence is also a big part of hitting, once you break the downward spiral, you might hope to see some swings make contact, too. And if you've drawn the infield in a bit, hits are more likely even if they don't have a lot of "pop" yet.
To do this most effectively you should separate them by 3-4 batters in the order. It's not often you'll want to bunt back to back, so put some space between them.
Also, be sure the top and middle guys in your order has to bunt when it's their turn, too. One of the best experiences my son had was when he got to his 13u team. He still batted cleanup, but if he came up with men on 1st and 2nd and no outs, he got the bunt sign. The message was: the team is more important than ANY one player, even the big slugger. This has the added benefit of having your struggling players feel like they aren't being singled out, they are only being asked to do what every other player would be asked to do in a similar situation. And it keeps your stud guys from getting their egos too big -- which will help curtail their natural tendency to ridicule their struggling teammates.
You can also reinforce this by devoting substantial practice time to bunting drills disguised as contests, situational hitting in batting practice, and contests among groups of the team in practice (3 groups of 4 or 4 groups of 3) where points are awarded not based on deep hits, but bunts and situational hits. Winners get an extra treat after practice!
We once had the typical cycle where we batted all our roster, but scored only when the top of the order came around. If they had a bad day, we would lose.
After we got more into "small ball", we broke open more games. Hitting feeds on itself, so we caught fire more often. Everyone got into the act. We still got bombs from the sluggers, but overall we put up a lot more runs. Sometimes we would just get one here, two there, next thing you know it's the fourth inning and we had 6 runs instead of the usual 1 or 2. We could win a 6-4 game where we used to lose 4-1. Or, if we got a big rally, instead of a good win it became slaughter rule time.
Most youth teams are formed by coaches who are looking primarily to advance their sons, and they recruit other players mainly to act as the supporting cast. If you develop the mentality that everyone is expected to contribute for the good of the team as a whole, you will blast those teams out of the water.
