From the creator of LeeDroid:

Q: How do I remove /system applications that I don’t want or need?

For the above there are several options:
Please take care when deleting HTC proprietary apk’s, there are a lot of dependancies in HTC ROMs…ALWAYS PERFORM A NANDROID BACKUP FIRST!
Option 1: Remove them from the zip prior to flashing the ROM, this is best done with either Winrar or 7zip, DO NOT EXTRACT THE ROM, simply navigate to the folder within the zip and delete the apk’s.

Q: I need ringtones/ notification tones on the system.

The best way to do so is before flashing open the zip (donot extract). Go to /system/media/audio – Drop your .mp3 into the respective folders.
Remember > You have not extracted the .zip, so once you drop it and close the zip, it will be there. Now flash as normal.