Hi @NateRogers1
Im going to make an assumption that you are using ArcPy and the arcpy.UploadServiceDefinition_server() function, there is an in_folder parameter you can use.
arcpy.UploadServiceDefinition_server(sd_output_filename, server_url, in_folder_type="EXISTING", in_folder="NAME OF FOLDER")
If my assumption is incorrect, you can share some code for assessment.
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