Rolling out: tenant admin tools to connect existing SharePoint team sites to new Office 365 Groups

TonyRedmond - Yes you can sync project online sites with the OneDrive sync client

And for the discussion about connecting site collections - yes only top level site collections are eligible to be connected to new Office 365 Groups.  While those site collections can have subsites, the Office 365 Group created will point to the site collection as it's SharePoint resource.

Generally, if your top level site collection has a site mailbox, connecting it to a new Office 365 Group with this feature and then moving mails over from the site mailbox to the group mailbox is a reasonable approach.  Adding Mohammad Sarosh if he has any additional comments.  If the site collection has subsites that have their own site mailboxes, those subsites will need to be migrated to top level site collections in order for them to take advantage of Office 365 Group capabilities (including group mailbox). This should be a top consideration for Project Online sites.