You should be able to ask for a private baptism for both children. Most parishes will have infant baptisms at least once a month in a separate ceremony, or some will also do them during a regular Mass. So your daughter could be baptized just about anytime. As for your older child, even after going through RCIA, he may be able to have a separate baptism at a private ceremony or another Mass. You may be able to look up information about this, or just ask the priest directly if he'll allow it.
As for taking the kids to Mass, once they are baptized they are part of the church, and should be attending Mass anyway. Now is a great time to get into the habit of going every Sunday and getting the kids used to it. Plus, if your older son receives First Communion after the RCIA process (not sure if he would, but he's at the right age for it), he would be required to attend Mass every Sunday and Holy Day, just like an adult.
Hope this helps! Prayers for you and your family.