They have a dock for the phone while wearing the extended battery but that may not work for a case or protective cover.
I purchased the Desktop dock during a sale last year. The cove I use has to be removed to place the phone in the dock. This occurs with both the standard and extended batteries.
I'm most definitely NOT a VZW employee. If a post answered your question, please mark it as the answer.
Thank you for contacting the forums! I will be more than happy to suggest an accessory to suit your needs.
The HTC SKU/Part# HTC6400DTC Dock Charging Station
Fits with Xtended Battery; Integrated battery dock to charge spare standard or extended battery! and you should be able to leave on your portective cover.
Please click on the link below to view this great accessory: http://www.verizonwireless.com/b2c/store/accessory?action=refineByCategory&categoryId=18