Hi, and welcome to the Microsoft Learn community.
It's not possible to sync files from two computers to the same OneDrive account and keep those files separate unless you place them in different folders. The Desktop, Documents, Pictures, Music, and Videos folders will merge. If you use a different account for each computer, you can keep the files separate.
You can utilize the Files On-Demand to select specific files to "Free up space" on each computer. Additionally, you can choose which folders you want to download to your computer by using the "Choose folders" option. However, this option is disabled for the Desktop, Documents, Pictures, Music, and Videos folders.
https://www.youtube.com/watch?v=i-tRV1q5BEU
Craig