It seems there is no way to add certificates in the standard mail app, which makes my private mail server useless.
How do I add the CaCert root certificate in my Firefox Phone?
At the moment, when I try to connect to my server I get the error
warning: TLS library problem: 15511:error:14094418:SSL routines:SSL3_READ_BYTES:tlsv1 alert unknown ca:s3_pkt.c:1261:SSL alert number 48:
Unfortunately this is not possible at the moment directly in the email app. Bug 874346 tracks the issue, but it is dependent on some platform bugs before it can be fully addressed.
In the meantime, the "User Story" section of that bug describes some workarounds that may help in some cases.