Yes, the agent will download patches from the Distribution Server if the option is set in the Agent Policies regardless on how the Deployment Template is setup
You will need to setup the IP ranges for the Distribution Servers, the following should help: How Do I Use A Distribution Server
You cannot setup an agentless scan to skip machines with agents installed on them. Rescheduling the time of the scan/reboots would be your only option at this point.
Please let me know if you have further questions.
My next question is if there are no listings for certain subnets in my IP Range, will the patches automatically fall back and use the console?
When using IP ranges in the Distribution Server Group setup, you can set a backup Distribution Server. I would suggest creating a Distribution Server on the Protect serer and then using that as the backup.
Most customers will use the the folder Protect is downloading patches to limit file duplication on the Protect server: C:\ProgramData\LANDesk\Shavlik Protect\Console\Patches (make sure you use a UNC path in the Distribution Server settings)
You can choose a different location in Tools > Operations > Downloads if you need to store the patches on another drive.