Don't know which distribution you are running, but I'm running Front Accounting on port 9101 under Ubuntu 9.10.
This link provided details on how to get the SSL self-signed cert installed and running on Apache2 (you should be able to select the steps you need if you are using a CA cert instead). http://www.tc.umn.edu/~brams006/selfsign_ubuntu.html
To the best of my memory, I didn't make any changes to Front Accounting other than during installation when asked for the URL, which I changed to be something like https://myserver:9101. I have Front Accounting as the only app on that port, but you should be able to configure based on the link above for whatever structure you require.
If you need more detail, let me know and I can forward some snippets from my system.
Brian.
One quick note: even if you've made all of the changes to the Apache2 files and have the SSL certs available, I had to complete the step #3 (a2enmod ssl) from the above link to make sure SSL was actually enabled on Apache2.