Suppose you have created a job and scoped to multiple web application.. the job should be smart enough to pick up the correct setting you may have added in the config file.. below is the code to get it..

// get the settings 
System.Configuration.Configuration myConfig;

//myConfig = WebConfigurationManager.OpenWebConfiguration("/", "SharePoint_500");
myConfig = WebConfigurationManager.OpenWebConfiguration("/", this.WebApplication.Name);

if (!myConfig.Equals(null))
{
       this.connStrFromAppSettings = myConfig.AppSettings.Settings["ConnectionString"].Value;
       this.CUSTOM_SITE_TEMPLATE_NAME = myConfig.AppSettings.Settings["CustomSiteTemplateName"].Value;
       this.SITECOLLECTION_URL = myConfig.AppSettings.Settings["SiteCollectionURL"].Value;
       this.BUFFER_SIZE = Convert.ToInt32(myConfig.AppSettings.Settings["BufferSize"].Value);
}