I don't want to get too specific, but lets say that I went to a really shady tax preparer and instead of owing taxes I got a very large refund and the lengths the preparer went through were very shady. I implored him not to do that, but ultimately I was in a bad situation in a very bad neighborhood.

So he filed it and I got the refund and cashed the check but I haven't spent any of it because I can't bring myself to.

I really want to file an amended return and pay back all the money and do my taxes legitimately.

My fear is that I turn around and try to do the right thing and get in trouble for it.

Does anyone have any advice?

In general, if you believe that your filed and accepted tax return was accurate to your best knowledge, you may not need to amend your return. Basically,there is no statute of limitation in filing 1040X/ your state amended return(if you need to file it also) you MAY amend your tax return any time. It doesn't matter whether you end up owing taxes or have additional money due to be refunded.However, this is NOT your situation but before amending any tax return you should always wait until you receive your refund. Otherwise, because you will have 2 returns in the IRS system ,the original return and the amendment, the IRS could cross at the IRS if you are reporting/amendimg SCh C income and cause a delay; aslongas Odds are you are going to OWE when you file the amended return. Then you need to pay interest/ failure to pay penalties. in general, just for reference, to claim a refund, you must file Form 1040X within 3 years after the date you filed your original return or within 2 years after the date you paid the tax, whichever is later. Returns filed before the due date without regard to extensions are considered filed on the due date.
you cannot efile it because the IRS does not allow tax amendments to be efiled. Therefore, you will need to mail your completed, amended return to the IRS in order for it to be filed