The Auto-Upgrade feature is most likely the least-taxing on your network. The Auto-Upgrade feature will use a Delta file to upgrade the client, so it is very small. Since your are upgrading from RU5 to RU6, the Auto-Upgrade delta system has been improved to be dramatically smaller. Before, the upgrade included a delta of the base AV Definitions -- which was totally useless. Now the delta only includes actual code changes -- don't quote me on it but I believe the delta was under 15MBs -- not sure though.
Also, unlike the MR4 to RU5 upgrade, the RU5 to RU6 upgrade should not cause a momentary network disconnect during the upgrade if you have the FW product installed (highly recommended).
And, as Brian81 already mentioned, you can schedule the upgrade to happen over several days to reduce network load and/or IT load.