The best practice is to use vCenter connection rather than connect to the hosts directly, but the second variant would also work.
Additionally I'd suggest you to install Veeam backup server on the remote site, which hosts your source VMs, and see whether you have any speed improvements. You can have a look at Pros and Cons
of installing backup server at different locations, to see what suits you best.
And remember if you choose to have backup server on the remote site you will be able to manage Backup deployment easily via Enterprise Manager console.
As for the issues you're experiencing with the product don't hesitate to contact our technical support team and ask for assistance.