Print checks and custom forms with PHP
You can try to run Cups server with your check printers connected to it. Cups server communicates with it's clients over IPP protocol.
You can create IPP printing job right from php using http://www.cups.org/articles.php?L545+TNews+Q
Printing jobs have attributes - media size is one of them.
So, this way user's OS won't print anything. User will just POST some query to http server, and php will create print job for cups server with media-size and some other attributes.
One of my clients uses tcpdf to print all of their checks. All of their checks are standard U.S. Letter sized.
As Dagon said, you can't control users printers from a PHP application - so instead how about you force them to use particular size checks? The full letter size checks my client uses are perfect - all of the year-to-date/deductions/tax stuff printed at the top and then the actual check at the bottom. They all go through a folding machine after printing so they can be mailed. (Employees with direct deposit get printed check stubs this way)