As you say, QT Creator is available under free software licenses (GPL and LGPL) that allows you to creative derivative works.
Forking this project to create My App Name is to create a derivative work.
The license requires you to make it clear that your My App Name is a fork of QT Creator (so that nobody that uses your version will believe that they are using the original). You are also required to preserve the original copyright notices and authorship attribution (so that nobody that uses your version will think that you wrote it from scratch).
The reasonable way to to this is to make sure that your IDE is clearly branded as My App Name, and that you put additional copyright and attribution information in comment blocks in the files that you change.
Their is no requirement to change file-names and class-names when you do this. You may do this, but my recommendation is to change as little as possible, to make it simple (by means diff or similar tools) to separate your real changes and additions from the original code.