I would be happy to provide some ideas for coordinating lesson plans.
As indicated in the introduction to kindergarten lessons, the CHC materials were developed for individual teaching. You present the lesson briefly and then your child continues the lesson independently. Then you work briefly with the next child and so on. It may be best to work with the youngest child first to get that child engaged in the lesson, and then work with the older children. It is vital that you spend the time with them to introduce them to the new material and answer any questions so they do not become frustrated trying to figure it out on their own and possibly learn the material incorrectly. And this is precious time that you probably already realize you will never regret spending with your boys.
There are checklists within the lesson plans to help you prepare for the week. This preparation is necessary so that you are ready to begin right away when school starts. Children quickly lose interest when the lesson must be delayed although they themselves are ready to go. In addition, the core subjects are highlighted in the lesson plans. You will want to focus on these and then add in the other subjects if time permits. At this age, school should not take up the whole day. If you are, for whatever reason, unable to get past the core subjects at first, be at peace. One of the advantages of home schooling is being able to move at your own pace according to the natural rhythm of your own family.
Try to establish a daily routine that fits your family. Children like knowing what to do and when to do it. Be patient until they learn the routine. For example, your boys probably have other activities to do besides school. If they complete a lesson and you are not free to present the next lesson for the day, then they should know what to do while waiting. That may mean tackling a chore, entertaining the baby, working on a practice or review drill, working physical fitness skills, or doing artwork or music practice. You can create a list of additional independent activities for your boys who can read and create a picture chart for the kindergartner. These charts and lists may be laminated for use again and again.
Keeping separate folders for each child is a wonderful idea. You can keep their lessons and charts in their own folder. They will know where to place completed work and what to do next. Even if a child cannot read, if he sees crayons and a coloring page or a puzzle in his folder, then he will know what he can do while waiting for his next lesson. Depending upon how much material you want to keep together, you may prefer to use sturdy boxes or trays instead of folders. Your boys may enjoy being surprised at what items you set in place for them to do.
You mention not being able to group lesson plans by week. That may be difficult, yet it is also useful in that you will not inadvertently mix up the lesson plans and the lesson plans remain with the supplementary material. If you prefer to group the lesson plans by week, perhaps you could make copies for a few weeks to determine whether that method is more convenient for you.
So advance preparation, organization, and an established routine may be the keys for the right proportion of school work to your day. If you find that something is still lacking, your older boys might be able to help you come up with more ideas for a smoother school day. Sometimes something very simple can make a big difference. I remember my children suggesting some excellent ideas at an early age, and I imagine that your boys will be a great resource.
May God bless you and your family. Have a happy and productive school year.