Is there any way to decide shipping methods on the checkout page depending on current store?

For example:
 If **storeview A** then show only Freeshipping. If **storeview B** then show only Flatrate.

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I am using IWD onepage checkout extension. </br>

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In System > configuration > shipping methods : </br>

I have set No to Enabled for My 2nd Website but, That method is still displying on Checkout page.

[![enter image description here][1]][1]


  [1]: https://i.sstatic.net/sr7tZ.png

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Current settings are as follow: </br>

Default Config : Flatrate > Enabled : No <br>
Website One : Flatrate > Enabled : Yes [Default checkbox is not selected] <br>
Website Two : Flatrate > Enabled : NO [Default checkbox is selected] <br>