One option is to import all the Images into OMERO as separate images (as you have done already) then assemble them into a Plate using the Dataset_To_Plate.py script.
There’s a brief description and demo movie of the script at http://help.openmicroscopy.org/scripts.html#utility. It’s a bit dated and shows the workflow in Insight client but this is still the same in the current webclient.
You just need to put your orphan images into a Dataset, then select the Dataset and launch the script. In webclient now, you launch scripts using the 2-cogs button in the top tool-bar.
This technique uses the naming of the images to order them. They are added to the plate in that order, going column-first OR row-first. Maybe try it with a small number of images first.
Another option is to try and assemble the images into a Plate before import to OMERO using OME-XML, but this is a bit more involved, so try the script approach first.
Hope that helps,