You can set giving limits for individuals and another one for organizations. You can also set separate limits for every org type if you wish.
To set these limits, just go to Finances, Setup, and click the Contribution Limits tab.
The warning system still warns you when you enter a donation that will push the record's total for the period over your defined limit. This warning system has been rewritten to look for the limit for that specific entity type (e.g. individual, PAC, Union, etc) .