will it still snipe at the y price which is more than the x price in myEbay?

Greetings,
Confusing, but I believe the answer is yes.

JBidwatcher places the bid that you’ve given it as a snipe bid, no matter what. Even if it’s too low, or if you’re already the high bidder. It tries to place that bid at the snipe time before the end of the auction, ignoring the state of the auction. There are lots of reasons for this, but one of the core reasons is it makes the logic a lot simpler. ;)

— Morgan Schweers, CyberFOX!

Are their any work-arounds for this?

I just accidentally set up a bid at X using jBid when I meant to setup a snipe at X. I’m afraid that if I now setup a snipe at value Y…. I’ll be outsniping myself. Is there anyway to fix my error since I would use jBid for both?

It’s impossible to bid against yourself – all that will happen is that your maximum bid will be raised. Remember it’s the person with the second highest bid who determines the final price (their bid plus one bid increment); the maximum bid only determines who ends up paying that money. If you have already bid the maximum amount you are willing to pay then there is no point sniping on it too.

Just to add to what has been posted.
I think the easiest way to think about all this is that a snipe is nothing more than a normal bid, it’s just timed to go in seconds before the auction ends to prevent someone from being notified in time to outbid you (unless they already have a higher maximum bid entered).
If you use the ‘bid’ function on JBW, the bid goes in at the time you place it; if you use the ‘snipe’ function, JBW places the bid (or tries to as best it can) the number of seconds before the auction ends that you specify.
As Laurence said – ebay prevents you from bidding against yourself and since sniping is the same as bidding (just before the auction closes), ebay will also prevent you from sniping against yourself.

Thank you Laurence and krs99!