I'm in the process of buying a new (to me) motor for my boat. It's a 2014 250 Pro XS with 178 hours. The hours are all light and it's in good condition. There is two years of warranty left on the motor. Does anyone have experience with aftermarket warranties or upgraded purchased mercury warranties? I really want to be sure I'm covered in case things go wrong.

I would definitely go thru Mercury for any extended warranties. Talk to you dealer to see what's available.

You said there are two years of warranty remaining, who offers the warranty? I don't know of many after market warranties so I'm assuming if it's a 2014 engine, the original owner purchased the 5 year Mercury plan if you say it has two years left. You need to find out if it's the Gold or Platinum Mercury warranty. Makes a big difference.

I have a 2014 Mercury 115, 4 stroke I just purchased the additional platinum MPP plan on. Here is my advice for you. Get the serial number off of the motor and call Mercury. At least on my motor, the factory warranty expires 3 years from the original date of purchase, and Mercury can tell you when that was. Additionally, they can tell you if the original owner bought an MPP plan (Mercury product protection). The gold will cover all the mechanical items, and the platinum will cover all mechanical and electrical items. The platinum should be the exact same as the original warranty as far as coverage, but they can't call it a warranty because you have to pay for it. If the owner bought an MPP, you have a limited time (30 days I believe) from the date on the bill of sale to have the MPP transferred to your name. There are instructions/paperwork from Mercury on how to do this. Additionally, if the motor is still under the factory warranty (3yr) and under 500 hrs, you can buy the MPP plan or upgrade an existing plan if you choose. There is some fine print that you can't buy an MPP if you use the motor for business (aka you're a guide). Not sure about if original owner was a guide, so if that applies you may check.

As mentioned above there is a big difference between Gold or Platinum warrantee as to what is actually covered. I would not even consider an "aftermarket warrantee" from another company. That being said the extended warranties direct from Mercury are ridiculously expensive. Thousands! I have not had a single need for warrantee work on my 2013 XS 250 but have heard from more than one mechanic that Merc does NOT pay "like a slot machine" often on the warrantee work when needed. Never wanting to actually cover the repairs. It's as if the warrantee's are sold for the profit of Mercury Marine! I never pay for any extended warrantee on my vehicles and I would not on my boat engine either because the chances of them paying off are not in my favor(that's the aforementioned profit). I take the risk by basically "self insuring" myself and saving the money. It is a gamble with the mathematical odds in my favor that usually pays me instead of the manufacturer. If there's no way you could afford the unlikely event of say a blown power head than don't take the risk. If you foresee selling your boat during the warrantee period it does though add a lot of value to your boat because many people are afraid to purchase a used boat without it still being under warrantee. To the original question: you can extend your Mercury warrantee to any of the longer warrantees at any time as long as your present warrantee has not expired. All you have to do is contact Mercury direct. Did I mention it's expensive? :-) https://www.mercurymarine.com

I also have a 2014 250 Pro XS. I would not even consider running this engine without Platinum Product Protection or insurance ( do you know what a new powerhead costs?) You need to purchase before the original "3" year warranty expires, not the extended. The Product Protection is a Mercury retail item, so dealers have the option to give discounts. I have never had a claim rejected in all the years I have ran Mercurys(a lot depends on the dealer).
An option is to insure your boat with a company that offers full mechanical coverage. A friend had a 250 powerhead fail and his insurance paid in full to replace the powerhead. He has Travelers Insurance.