FileVault for a 2-partition system

My MacBook disk has 2 main partitions:  OSX and Data.  Lion is installed to the OSX partition and my user account was updated to point to its Home directory on the Data partition.  My expectation is that when I enabled FileVault, only the OSX partition was encrypted.  I would like the Data partition to be encrypted as well.  Based on a little research, it seems this can be done with Disk Utility by reformatting the Data partition as Mac OS Extended (Journaled, Encrypted).  I would obviously first need to backup all my data and erase the contents of the Data partition.  I probably need to temporarily configure my account to point to a Home directory on OSX (but that will cause problems with all my apps in Data/Library... ?).  Then I would restore the data back to the encrypted Data partition and then point Home directory back to Data. 
Is this what I need to do?  Will the integration be seemless, or will the Data partition have its own separate encryption key that will make it difficult to be setup as a Home directory??
THANKS

Fair question.  I've been using this strategy for years and years, beginning on Windows systems then carried over to OS X.  There are probably a number of reasons, but in practice the main reason is it facilitates my backup process.  I handle backups of my system drive differently from my data.  I use SuperDuper to create an image copy, which is easy to restore from.  I rely on Time Machine to backup my much larger data files.  I backup my system drive less frequently than data, since it doesn't change much, but I back it up completely.  A SuperDuper image of a consolidated drive would be 100s of gigabytes and wouldn't allow for a quick restore.  Here are some additional comments on that http://lnx2mac.blogspot.com/2010/08/multiple-partitions-on-os-x-pros-and.html.
Why do you say separating system from data on 2 partitions on the same disk is not a good idea?  I would prefer to have 2 disks for this purpose, but I'm working with my MacBook.
I successfully addressed the problem of this post following the easy guide in the link in the second post.  I wouldn't necessarily recommend this workaround for all users, but it seems pretty simple and safe as long as you are careful.

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