It depends on the encryption system that you use. Some use the password as
the encryption key and others use a encryption key file and separate
password.

I use Cryptkeeper from the Ubuntu repos. I have an encrypted folder on an
external drive that I can use on any distribution that has Cryptkeeper
installed. The way it works is that it creates a hidden folder where even
the file names are encrpyted and a folder of the same name that is not
encrypted and not hidden with no files in it.

Let's say that my folder is called Private then it creates and encrypted
folder called .Private_encfs as well as the one called Private. Everything
is inside .Private_encfs and nothing should be in Private. The files in the
encrypted folder all all alpha numerics and unreadable. When I load
Cryptkeeper and unlock it then Private appears to be full and I can work on
the files and add and remvoe files in the Private folder. When I lock and
shut down Cryptkeeper then Private once again appears to be empty. You can
even delete the Private folder and all you will have to do is create a new
one in Cryptkeeper and use the same encryption key as your password.

I have to set up Cryptkeeper on each distribution to use that folder by
pointing to the encrpypted and hidden folder on the external drive. The
password has to be the same because it is part of the encryption algorithm.
Once it is set up and the password is given then I see the encrypted files
in the folder that was previously empty. I don't think that there are any
files ever really in it because if you put a file in it when it is
unencrypted but visible then you cannot use Cryptkeeper until that file is
removed. In other words this folder is only for use in Cryptkeeper.

It works for me. You cna have several encrypted folders on different drives
or partions with different passwords. I have also used Truecrypt but it is
proprietary and not easy to set up on some distributions. The down side of
Cryptkeeper is that it is available for Ubuntu and other Debian systems, but
will not work in RPM systems and I often have RPM distros install as well.

If you want to do this from Windows and Linux then your best bet is to find
one that uses Truecrypt on both operating systems.