MikroTik

Is there anyway to use SSL encryption with IPSEC? If so how?
I plan on using this with a corporate network that has three different locations.

IPSec includes its own encryption schemes. SSL/TLS is more typically associated with client/server end to end security. What did you have in mind?

I need a secure tunnel between several offices and I am having trouble with MTU sizing and it is affecting serveral applications that we are using. We only have three location and MPLS seems a little extreme for our needs. I just want a secure yet low overhead connection that will not fragment packets due to MTU.

Does that make any sense?

Tunnels will tend to cause fragmentation but if you are having problems with a TCP-based application you can clamp the MSS on traffic entering/leaving the tunnel. That works well in most situations if using something like a GRE tunnel.