I like trays for starting young trees. You can put 9 seedlings in those trays you bought and trim their roots before potting them up, and put them on a tile in the tray too. I like to put these trays on the ground so the roots can escape and help the trees grow faster. After and year or two so you can pull them up and work their roots again and either put them back in the tray for a few more years or pot them up into their own container depending on how well they are doing. Young trees take a long time to make into bonsai and you want good roots, good nebari, good trunk, and good branching, all which you get by working the tree, but each time you do you slow them down, and you need to let the tree grow to get girth and taper, its all a fine balancing act that you always are learning from. Growing in the ground or on the ground so roots can escape can speed up the process quite a bit and allow you to work the tree more often than if it was just in a pot on a bench. Also the stronger a tree is the healthier it is and will resist disease and bugs more. There is no just one "right" way, it changes for everyone depending on weather, sun/shade, soil comp, species, and many more Im sure, just gotta find a way that works well for you. Try something and take notes. If it works well over another way then do that.
Good Luck,
Ed