It depends on what you need security for. Digital Certificates are can be used for authentication and/or for encryption.
It also depends on your existing design. I have found that breaking an entire systems integration into independent sub-systems based on the resources that are integrated is an excellent way of ensuring that your system will be maintainable as it grows in size and scope. This applies to your security architecture as well.
If you have not broken it down then your security will most likely be more of an on/off for the entire system.
I recommend that you read Chapter 10 of the AdminAnalysis.pdf file. One thing to keep in mind is that the digital certificates will be stored in certificate files that are password protected. If you use the same digital certificate in several certificate files then it will be more likely that access can be gained to one of the certificate files that subsequently can be used to gain access to the system. It comes back to what requirements you have for your security architecture.