No, you did it the correct way (BLS wants teams populated, so that's why the VACANTs). Easiest thing would be to mark the individual VACANTs as having quit (then, there is a function about deleting quitters) and I'd do those things first. Essentially, that's the only "tip" that would be of benefit--to remove the VACANTs first.
I do not have my BLS handy so I can't give the exact step but if you've used BLS, you may be able to get there on your own (and others will reply over time). But once you delete the VACANTs, then as you populate the teams, do so linking from the MBD as you intend to do. The Bowler ID numbers will be lower numbers as they will become available as the VACANTs are removed.
It's always a few extra steps getting a league going for the first time, but once it's set, you've used BLS prior to the MBD...you no doubt already have a decent working knowledge.
Always check, download, and install the most recent update of your software to ensure that issues may have been corrected.