Uninstall present BOINC through Control Panel\Programs\Programs and Features\
Download the 64bit installer from Berkeley and start it.
In the third screen in the installer, click Advanced.
Change the path for the Programs directory from C:\Program Files (x86)\BOINC\ to C:\Program Files\BOINC\
Leave the path to the Data directory as it is.
Continue the installation.
All preferences files are stored in the Data directory. As long as you don't fiddle with the path, it'll stay intact.
The only change you have to make is the path for the programs directory, since the installer reads from the registry what the path for the last install of BOINC was and reuse that path.
The BOINC installer itself is just a 32bit Microsoft Installer file that contains a database which contains the BOINC program files. It cannot read if the files contained in itself are 32bit or 64bit, and therefore the installer cannot adjust the path to the correct programs directory for you, you will have to do that by hand.
Windows itself states that you cannot start 64bit programs from the protected C:\program Files (x86)\ directory, as this is the programs directory reserved for 32bit programs only (hence the (x86) addition).
Lastly however, it doesn't matter what BOINC version you run, the 32bit version will run 64bit programs just as much as the 64bit version of BOINC does. The projects check the operating system that you run, not the BOINC version, in order to send you their 32bit or 64bit programs. The only difference between the 32bit and 64bit versions of BOINC is the amount of memory they can address.
Fighting for the correct use of the apostrophe, together with Weird Al Yankovic