Gina and I decided early on that we wanted our kids to sit through the whole church service. That was born out of a matrix of convictions I won't unpack here, but suffice it to say that God has blessed us and our four boys (ages 10, 9, 6, 4) all sit through church without incident.
1. It starts by not viewing our boys as a pack of wild animals. I'm serious about that. They have their moments and are certainly a playful bunch, but we have never bought into the notion that boys are just going to be de facto bouncing off the walls. Our working assumption is that they are little bundles of energy who need constant structure, discipline, and reward. If you assume that they "can't" or "won't" do something - guess what? You're right. So much of parenting is self-fulfilling prophecy.
2. We try to coach them on the way to church concerning worship - Who we are meeting with, what is going on, what is expected, etc. Think of it as catechism on the way to church.
3. With our oldest two boys, there was a lot of discipline in the beginning. And by discipline, I mean spanking. We had the most success using a glue stick (from a glue gun, not the preschool kind). If the kids got overly fidgety we would open Gina's purse and show them the glue stick. The warning worked most of the time, but there were many times that we pulled a struggling toddler out for a little time with the "rod." Our youngest two didn't require much discipline because they just mirrored the older brothers' behavior.
4. We don't allow TV or video games on Sunday mornings because we discovered it started them off down the "time to play" track.
5. We give them a good breakfast and bathe them.
6. We let them scribble when the sermon starts.
7. When they were young we brought a snack for them to eat during the sermon.
8. We made them stand during standing parts of the service so they could participate and stretch their legs.
9. We reward them for good behavior after the service. Food, video games, whatever. It all works.
10. We ask them after church what they heard or learned in church. We're not looking for a particular answer, it is the exercise that counts.
In short, we approach church just like we approach any number of other parts of our life with young boys. You have certain expectations, you prepare them for what you expect, you enforce behaviors with discipline / rewards, and you engage them at whatever level they are at to encourage participation. There is no real mystery, and your boys CAN do it, but it comes down to YOUR choices and behaviors as a PARENT.