Hi,
I would suggest the following Management Profile configuration (tab 'Discovery Options'):
1) Lower the 'Agent Priority' value from 'Highest' to 'Medium': this will make the agent process have less impact on server CPU and give priority to other (more important) processes, though discovery will take more time (still, this is a discovery tool and not a critical process);
2) Set a 'Discovery Time Limit' to a limited number of minutes: don't leave it at 'Unlimited';
3) If possible set a 'File Search Depth' value which will override whatever is defined in the Management Profile's blueprints;
4) Don't check 'Follow Symbolic Links' unless you have a good reason to.
5) Don't check 'Include Network Drives' unless you have a good reason to.
Other than this, I would prefer having multiple Management Profiles with fewer blueprints and run discoveries in turn, rather than having a single MP with many blueprints.
You must never add all blueprints (or even dozens) to the MP.
If you're using custom blueprints make sure the discovery criteria is specific enough so that the agent doesn't have to scan all filesystems.
Hope this helps.
Regards,
Tiago Santos