If you navigate to WIndow > Prefs > MyEclipse > Project Capabilities > Struts > Struts 1.2, you can see a list of all the resources that are added when you add “Struts Capabilities” and select “Struts 1.2”. You can remove all the elements from this list and add the 1.2.6 version that you wish to use instead.
If you are asking about an existing project, then just drop the updated JARs into your WEB-INF/lib directory. If you are upgrading from Struts 1.1 to 1.2.6 then you will need to manually edit a project file, otherwise if you are upgrading from 1.2.x to 1.2.6 then you should just need to update the JAR (and TLD if you have them) files.