As the parent of a child with a learning disability in the Catholic school system, I suggest you look very closely at the school you are considering. Some Catholic school are not set up to handle children with an LD. They can only teach to the 'middle of the road' child.
My dd was spending 3-4 hours a night doing homework in 1st grade (this same homework took other children 10-20 minutes to complete). I spent HOURS sitting at the kitchen table with her, working through each problem, making sure everything was done, completely, placed in her folder, and ready for school. Her brother (2 years younger) also spent HOURS at the table - coloring, playing with playdough, painting with water, whatever - because my dd *needed* my attention. I know he was young but I explained that he had my time during the day, so right now I *had* to help his sister. I think your two boys could learn this same theory. "A needs my help right now, so I need you to both play cars nicely here on the floor." Or duplos or whatever. It isn't fair to your daughter.
My ds actually was ahead of the game when it came to school because he spent SO much time listening to me work with our dd.
Our 1st Catholic school did not have IEPs, nor did they support anyone with an LD. It was the parents' job to do that. Their attitude - if the student can't keep up, they need to go elsewhere. They were also big into worksheets -- lots and lots of paperwork, 'busy work' as one teacher called it.
We have moved to a different state and chose our new Catholic school, partly based on the LD program they have in place. It is AMAZING the things *any* school can do for a child, if they care too. She had a classroom partner to help make sure EVERYTHING is in her backpack for at home. They use assignment books (initialled at the end of each day). They have 2 learning consultants to help the kids learn coping skills specifically based on the child's diagnosis.
My point is... don't think because it is a Catholic school that they will be better for your daughter. Stricter isn't always better.
Should you continue the afterschool program? As a parent who's after-school time was at a premium, because I knew I needed to spend a lot of time with my dd, I limited her activities based on what we had to accomplish at home. If you are unable to give her more of your time at home, what difference does it make if she is doing crafts at school 1 on 1 with an adult, or playing at home?
Once you have a diagnosis from your doctor, by law, your school is required to provide more assistance (whether it is preferred seating in the classroom to oral testing) based on that diagnosis. Medication does not have to be a part of this solution. If it isn't, you do need to do other things to help. Medication was not recommended for my dd, but I feel like I have completed 1st through 5th grade all over again! She is currently in 6th grade, doing wonderful and, for the first year, I don't feel like I am actively relearning/reteaching everything to her. All of the hard work is really paying off.
PM me if I can help in any way and good luck!