Thank you for your question. It sounds like you might not be very familiar with WordPress Multisite? That would be the first place to start. Here are instructions to follow for setting up Multisite:
The Cloner only works in multisite mode, and multisite works from a single database. You only have to install / configure it once. The Cloner handles the rest.
You will probably want to drop the www from the domain names. It is unnecessary and ugly when it comes to working with subdomains.
The general process will be:
1. Setup and configure WP Multisite on main.com
2. Since you want to use subdomain mode of multisite you will have to make sure your host supports a wildcard DNS entry and that this is setup correctly.
3. Create your template site in WP Multisite. You can use the normal WP Network admin tools or the Cloner to create 01.main.com.
4. Use the Cloner to copy 01.main.com to 02.main.com.
There are lots of tutorials out there on Multisite, but you'll need to understand how it works really well to be able to use the Cloner to your best advantage. If you are determined, you can totally figure it out. But if any of this sounds scary to you, then the Cloner might not be the best tool for you to dive into right away.
There are lots of quirks to running and managing a WP Multisite Network to require a lot more specific attention than standard WordPress. But there are tons of resources out there and if you take it one step at a time you can definitely learn as you go.
Once the new sites are cloned / created in the network, they are completely unique sites and can be modified separately from other sites.
Hope that helps!