This is a three step prep.  When you want to convert from one style of decoder to another, this procedure might work well for you too.

A clip type decoder holder is a convenience for the locomotive manufacturer.  The first thing I do is to cut the “ears” or clips off the decoder holder with a pair of flush cutters.  Next I might file the cut area flat if I intend to use Walthers Goo, silicone gasket sealant or rubber cement to attach the new decoder that way.

I like the idea of leaving a little space under the decoder if there is room but it is not necessary.  The yellow line shows where I cut off the clips.

The next picture shows how I have used Kapton tape to secure a Decoder Buddy to the clip-less decoder holder. The fine red lines show a profile of the clips to be removed.  These two locomotives happen to be Atlas but Athearn, Athearn Genesis and others use or used the same method of attachment.  
 

This has turned out to be a very workable and durable method for conversions.