This page covers the basics of how to print a check, and also the print alignment and other features found under the Merchant - PDF Settings menu.
NOTE: The moment you click on the Print icon - which you do to view and print a check - the icon changes to grayscale. This feature can be used to indicate which checks you have already viewed and presumably printed.
Never Viewed:

Previously Viewed/Printed:

Obviously, checks are very highly formatted. Certain data must be placed in exact locations. There is a setting in the Print Dialog box of Adobe that can alter the correct placement of this data. When the Adobe Brpwser helper launches the document into your browser, the Adobe toolbar will appear just above the actual check document.
Click on the Print icon on the Adobe toolbar - not the Browser's Print icon. That will launch the Adobe print dialog box (see image below). On the bottom right area of the dialog box for older versions of Adobe Reader, there is an option for "Shrink oversized pages to paper size." Make sure that option is UNCHECKED!. Adobe should remember this setting for future printings - but it is a good idea to double check each time you print a check. Newer versions may have the option for Page Scaling in a drop-down box. Make sure that is set to None.
On some printers, using the Auto-Rotate and Center option in the Adobe print dialog does the trick, on others - it throws everything way off. Again, depending on the printer you use, you may have to play with the settings to get the positioning within acceptable margins.
Also, depending on your printer, you may receive a warning that certain areas of the page are outside the printable margins. Ignore all such warning and select the option to continue.
However, because all printers and printer drivers vary, the above settings may not put the critical MICR line where it needs to be. Or, due to the way the printer grabs the paper, the entire PDF image may print too high or too low.
The Merchant - PDF Settings menu allows you to fine tune the exact placement of the PDF image to your exact printer by adjusting it up, down, left or right by increments of 1/100th of an inch.
That page in the Control Panel has very detailed instructions on where the MICR line should fall and how to make adjustments.
NOTE: On a basic level account, you have the choice of printing a single check with 2 voucher copies of that check on a sheet of paper or check stock or the option of printing just the negotiable check with NO voucher copies (See NOTE below). On PRO level accounts, you can also choose to have 3 different checks print on a single sheet of check stock and have the option of the two most popular sizes of business size check stock.
Also, if using check stock (which is highly recommended), there is no reason to waste check stock when trying to adjust the print alignment. Just print the test checks on plain paper and then hold that print behind a piece of check stock and in front of a bright light. The print out should show through enough to indicate if its where it needs to be (assuming the check stock has the MICR |: watermark symbol to show the idea location).
NOTE: Not every user needs or wants the voucher copies of the check - and printing them was a waste of check stock (if you used check stock with three, 3.5" checks on each sheet) and toner.
Now you have the option of printing just the actual negotiable check with NO voucher copies. This allows you to print 3 different checks on a single sheet of check stock (again, if you use check stock with 3 checks on a page instead of just a top check with two blank vouchers below).
To do this, simply print the first check, separate it at the 3.5" preforation and when ready, use the remaining portion for the next check (you may have to feed it through the manual feed slot of your printer). NOTE: depending on the printer, you may have difficulty with the final (bottom) section of check stock since it will be only 4" tall and may not be grabbed by all the paper rollers.
This option is also available to Pro level accounts for printing single checks. Printing 3 different checks per page of check stock (all at once) is automatic when using the Batch feature built into the Pro level accounts.
In your control panel, go to the Merchant - PDF Settings menu to select this option. Make sure you scroll to the bottom of the screen and click the button to save your changes.