When you use Wad Manager, it does not ask you what IOS to install TO, you don't install things to IOS's. It asks you what IOS to USE to install the wad. The IOS you use needs to be any IOS that has the trucha bug intact. If you have any cIOS installed beforehand, your IOS249 should have the trucha bug in it.
If you are on any firmware higher than 3.2 and have not installed a cIOS on your system, then you will need to use the Trucha Bug Restorer to get the trucha bug back on IOS36, and then use the cIOS rev14 installer and have that USE IOS36 to install and it will install to IOS249. Then you can use IOS249 in Wad Manager.