Hi,
Q. I'm looking at upgrading our Endpoing protection to the latest version, however I'm a bit confused about the upgrade path? Also is there anything I need to do to the cliens or will they auto update with the new install?
--> Please check supported upgrade path for both i.e SEPM & SEP clients, go through these articles.
Supported upgrade paths to Symantec Endpoint Protection Manager 12.1 from Symantec Endpoint Protection Manager 11.x
http://www.symantec.com/business/support/index?page=content&id=TECH192779
Supported upgrade paths for the Symantec Endpoint Protection client
http://www.symantec.com/docs/HOWTO81070
To upgrade clients you can use Auto upgrade feature.
http://www.symantec.com/connect/articles/upgrade-clients-sep-121-auto-upgrade-feature
Q. Also we are looking at migrating from Windows 2003 -> 2012 at the same time. Is it advisable to do it all at once, or upgrade SEM first then install SEM on the new server and switch over?
--> This question can be answered with best possible solution if you could provide following details
1) Total number of clients
2) Total number of SEPM's