Charter schools are public schools. They may have somewhat different programs or a specific focus that traditional schools do not, but they still have to comply with the same legal rules. That means they have to comply with the Individuals with Disabilities Education Act, Section 504, the Americans With Disabilities Act and other state and federal civil rights laws.
You may have noticed that charter schools often have strict rules of conduct, require uniforms, and have other differences from ordinary public schools. In the past, that has sometimes resulted in non-compliant kids being "counseled out," or discouraged from attending. In some cases, these included children with disabilities or learning issues. The law is very clear; counseling out kids with disabilities is unlawful. If your child has a disability, they still have every right to attend any charter school they otherwise qualify to attend.
Charter schools also have the same responsibilities as other public schools to develop appropriate Individual Education Programs and 504 plans. These lay out an appropriate education plan and a plan for ensuring full access to education. Charter schools also have to provide appropriate accommodations for children with disabilities.
If you've decided a certain charter school is the best learning environment for your child, what you need to do first is ensure that your child meets all eligibility requirements to receive an IEP and/or 504 plan. Assuming they do, sit down with your child and their teachers. Discuss some ideas for how best to meet your child's educational needs while helping them fit in with the school's culture and rules as much as possible. These preliminary discussions can give you a good grasp of what accommodations your child might need.
Then, finalize the IEP and/or 504 plan, if you're satisfied. If you're not satisfied with the plan and can't reach a better agreement with the school, consider talking to an education law attorney. While an attorney can be helpful at any step in the process, you'll definitely want to discuss your concerns if you can't come up with a satisfactory IEP and 504 plan on your own.
Every public school -- including charter schools -- has a legal duty to provide a free and appropriate education to each child. You and your child have rights.