If I select in the chart options for a VM the CPU Usage, do I measure the CPU of the virtual CPU of the VM or the usage of the VM on the physical CPU?
When you're looking at CPU usage it reflects what the VM is actually using on the host.
So therefore I do not get an alarm for CPU Usage (Warning 55%) although Taskmanager in VM shows 75% CPU Usage. If I check for the chart option for the VM the CPU Usage shows 53%
Is it possible to set an alarm based on the virtual CPU usage?
You could build a PowerShell script to check for this which could check the VM directly periodically.
Getting this info is a little tricky using PowerCli, but certainly is possible.
LucD has wirtten a good 'how to' guide here:
http://www.lucd.info/2010/12/03/hitchhikers-guide-to-get-esxtop-part-1/#more-2790
All you need to do is adapt his script by amending the intervals and amount of time to monitor for, adjust the counters used and possibly get the script to send an email alert or similar.
the only downside is that you need to connect direct to an ESX host, so if the VM gets moved due to DRS, you'll need to adjust the script.
good luck.