The problem with having both versions of Calibre (32 and 64), is the update notice you get (eg Update found 1.1.0) doesn't distinguish between these versions.
For example, I have Calibre 32 running ver 1.0.0, and then installed Calibre 64, ver 1.1.0. Now whenever I start Calibre 64 I get a message advising there is an update - which there isn't for 64bit Calibre. The update is for the 32bit version which I no longer use.
Personally, I really, really don't want to uninstall both and then install the version I want (64bit). I know I won't lose my libraries, but what about all the other settings in Calibre, the add-ons, custom columns, etc? The manual/user guide says the following which is slightly disturbing comments: "Note that restoring configuration directories is not officially supported, but should work in most cases."
I will give this a go and report back...
UPDATE - 10 mins later
It works
1. Back up the Calibre settings/configuration folder - it will be in your user folder - AppData - Roaming - Calibre (an ordinary copy to another location will do)
2. Uninstall both versions - it may not be strictly necessary to uninstall both, but it seemed cleaner somehow to do this
3. Install Calibre 64bit
4. Run Calibre when prompted - I cancelled all the prompts to specify settings like the location of library
5. Opening Calibre, even if you cancel as above, creates the Calibre settings/configuration folder
6. Close Calibre
7. Copy previously backed up settings/confirguration into your newly recreated user folder - AppData - Roaming - Calibre (replace all when prompted)
8. Open Calibre (64bit) and everything is where it should be - at least it is for me.
Best wishes.