Its not possible to deselect 64bit definitions , its by design
it will download for 32bit and 64 bit definitions.

there are chances if definitions are corrupt these folders might grow, do a cleanup following this document.
Symantec Endpoint Protection Manager 11.x is not updating 32 or 64 bit virus definitions
https://www-secure.symantec.com/connect/forums/no-notifications-no-email-notifications

in your network if your not using network threat protection , then you can just download only antivirus and antispyware  only
this feature can be set under
open sep manager
click on admin - sevesrs - right click local site -select properties
click liveupdate -keep the content revisions to 3
in the content types to download just select what is installed on your network, these settings should take care of the issue.
https://www-secure.symantec.com/connect/forums/sepm-unbelieveably-excessive-disk-usage

HI,

You can go to Admin->Server-> Highlight the local site and go to site properies.

In the liveupdate tab, check the number of content revisions you are keeping. Make sure that they are not more than 5.

Aniket

Thanks for your replies - however I don't have the disk space management field -

Do I need a MR to add this field?

Currently running Version 11.0.1000.1375

Thanks

I would strongly recommend upgrading to MR5, MR1 is a very old release and I believe you're overall experience would be much improved on MR5.  You can upgrade the server without upgrading the clients, then roll them to MR5 when you are ready.

 The only option available for you is to upgrade to the Latest version of SEPM.
Never set content revision to 1
https://www-secure.symantec.com/connect/idea/symantec-endpoint-protection-manager-should-not-allow-set-number-content-revisions-keep-1