Can I add increase the number of bays of the vessel to load containers?

Yes!

From the 2D View, BAPLIE Viewer Online automatically checks the data in the file to determine which bays, cells, and tiers are necessary. 

If you’re loading an incomplete file and need to add additional bays, cells, or tiers - you can now modify this from within the 2D View. 

Click on Settings, then Change Vessel Dimensions. Once you’ve changed the dimensions, you can load containers into the new bays either manually or from another file.

Please see this article for detailed steps.