There's a couple of ways you can do this.
First, bounce rather than merge the parts. This leaves you all the audio options available on the waveform.
You can highlight all the parts you wish to edit, right click and select the fade tab to the right of the edit window. Adjust to edit all highlighted parts identically.
Alternately, if you don't want to bounce the parts, you can assign them to either a buss or a VCA and use the automation available on those faders.
Hope that helps.