If you've set up your printer correctly, Quicken knows which alignment feature to try first. Generally, coarse alignment is used first on continuous-feed printers and for large adjustments of one line feed or more. Fine alignment is used for page-oriented printers and small adjustments of less than one line feed.
Once your checks have printed successfully, note the check position so that you can reload your checks to this position in the future. Do this even if your printer has an autoload or park feature.