It has nothing to do with S/MIME which is an email encryption setting. What you need to do is talk to your IT to find out the Mobile ActiveSync server information. However, I suspect your issue is simply the configuration. Typically, an internet facing ActiveSync server (that your phone talks to) must use SSL (https) to secure the communication. SSL requires a certificate. There are two types of SSL certificate: self-generated and public trusted. The former is what a lot of small company uses because it is free. The later requires a yearly fee to purchase a real certificate from publically trusted certificate authority (CA). Mobile phones all come loaded with common known CA root certificates so that any of the certificates issued by them will be recognized. However, this is not the case with self-generated certificates which is what OP encounters. Desktop Windows has work around built-in to let it trust those self-generated certificates easily. On mobile, you will have to import the certificate (preferably the root certificate) manually to the device to grant the trust.
All this could be avoided if your IT did the job correctly (by purchasing a real certificate).