An isotype control is an antibody with the same immunoglobulin isotype (e.g., IgG) as your main primary antibody but it doesn’t bind to a specific target. Isotype controls let you account for unwanted Fc receptor interactions, which can generate background signal.
For a conjugated primary, your isotype control should be conjugated to the same reporter. For example, you’d control for a primary antibody conjugated to FITC with an isotype antibody also conjugated to FITC. You can change isotype antibodies conjugated to FITC or APC.