My understanding in 2010 and the older 2.5 versions was that the group with the lowest groupid would win in the case of multiple groups applying templates that set the same template settings. Of course this makes no real world sense, just in a mysql programming sense. So the best policy is to always avoid applying templates via groups where the same template settings would overlap between defined template groups.
Depending on how granular you need to control your settings you may need to go to to the one group/template per setting config. I have been able to group the settings into group/template combination that make sense together and are exclusive. I have two different service brands so I have two separate searches/groups/templates that apply the different branding to the agent, pop up text, etc. Agents can only be in one group based on their contract level.
I apply Windows Updates nightly for workstations which allows me to have an single template/group for patch install window settings. If a client required that I only could patch workstations only on a single specific night of the week, this would require 7 separate template/groups one for each night of the week in addition to my current workstation every night patch install template/group based on the searches and the limit to checkbox is always set to remove agent that no longer fit the search results.
Items that can be set across all agents can be handled in a default group, but if you are going to EVER want to vary any of the settings you are considering in the default group you should not define them in a default group/template. For example, if you ever want to hide your agent during an audit for new or potential clients then the default agent visibility settings should not be set in the default group. Instead you should use branding group(s), even if there is just one that turns on all of the settings you would normally have enabled for your clients when they are not in an audit only state.
Also members of your template/groups should always be autojoined versus and dragged and dropped so that they receive your ongoing template changes. Template settings are applied to drag/drop agents upon their joining the group, or when manually applied through the group template Apply button. Autojoin agents have their template settings reset every 30 minutes when Labtech forces the group autojoins to run.
Java, Reader, iTunes and others - Audited, Updated, Verified, Ticketed and Billed