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Intuit can only assure compatibility with checks specifically designed for our system, Hillarylau.
On the Fine-tune alignment page, you can only move the alignment for the check amount. Nevertheless, we still have some steps that you can try to align your checks correctly.
First, you'll have to download and use Adobe Reader to control the printing. Next, set it as default PDF viewer for your browser. Then, print a sample check.
If you have further questions with this, just drop a comment below.