How to constrain tse on cyclone III board

Usually the tse sopc sdc file is enough. Then you only need to constrain your input clock and PLLs outputs, which drive your mac rx/tx clock ports.

I'm not an Ethernet guru but I think the extra FF in the preamble is not a problem, since the mac should discard symbols until it receives a complete the preamble sequence (and this eventually arrives correctly, isn't it?); when the preamble has been received the mac will receive the actual data payload.