Another alternative to using HTML to create the checks would be to create the checks as a PDF file which should give you alot more flexibility with the layout and printing options.
There is an amazing class called FPDF that will allow you to generate PDF files in PHP. It's very easy to use, well documented, and (best of all) FREE! I use it when I'm creating invoices and receipts in ecommerce apps and if I were coding what you're doing I'd use it there too.
Here's a link to check out:
http://www.fpdf.org/
Also, if you'd like to import existing PDFs (like maybe a couple templates with customized backgrounds for your checks) check out this addon to FPDF called FPDI. You can take any PDF file, import it to the class and start writing on it.
http://fpdi.setasign.de/