I dont think their is any way to peform the incremental backups on the Site collections level.
The Backup-SPFarm cmdlet creates a backup for the entire farm or
individual components within the farm. It can also be used to back up
just the configuration settings of a farm to be used as a farm
template for other SharePoint farms. If you want to back up a single
site collection, use the Backup-SPSite cmdlet.
When the url parameter is used, a backup of the site collection is
created. However when the backupmethod parameter is used, a backup of
an individual database, Web application, or the entire farm can be
created. If you want to overwrite an existing backup file for a site
collection only, use the overwrite parameter.
Updated: You want backup of the Web application.
You can use the backup-spfarm
Backup-SPFarm -Directory <BackupFolder> -BackupMethod Full -Item <WebApplicationName> [-Verbose]