application.cfc vs application.cfm

My CF version is 8 but since I came to this company and inherrited the codes, it looks like previous programmer did not use much of CF8 features.

I started to take advantage of CF8 features including cfc. One thing that I notice is all the existing apps. are using application.cfm and none uses application.cfc

I have sort of a portal web application where under this app. there are a bunch of different applications

The portal application has application.cfm that is encrypted so whenever I create a new app, I created my own application.cfm each with a different name set on the cfapplication tag

So it sort of to look like this:

Portal app

  application.cfm (encrypted)

     application_1

       application.cfm

     application_2

      application.cfm

     application_3

       application.cfm

I want to experience the CF8 application.cfc and from what I read, if I use application.cfc I can't use application.cfm because application.cfc replacing application.cfm and OnrequestEnd.cfm

when application.cfc is present both application.cfm and OnrequestEnd.cfm are going to be ignored.

My concern is, when I start creating application.cfc on my sub application, will the application.cfc ignoring Portal's application.cfm (the encrypted application.cfm) eventhough it is

on a much higher up in the directory tree?

So can i do the following without messing up the whole application?

Portal app

  application.cfm (encrypted)

     application_1

       application.cfm

     application_2

      application.cfm

     application_3

       application.cfm

     application_4

       application.cfc  <<< (?)