First keep in mind that while 25M for FastEthernet is still available slowly more and more there is a move to 50M with 2 bit known as RMII as
50M and RMII have simple implementation and clock is still relatively slow while the benefit of half the pin in multi-port is tremendous, and to some extend might be even easier for you as you have single source of clock and no more rx and tx clock each have its own ppm's.
Manchester is generally speaking used only in Fiber and not over cupper.
As for Manchester Freq since each bit is represents by two bits (0 become 01, 1 become 10) the Manchester frequency is double the Data frequency.
As for FastEthernet Cupper the freq over the wire as far as I know will be
100M from Mac to Phy let say using 25Mx4 Than in the phy after the 4/5 bit encoding 25x4/5 =125 Than after MLT3 125x2/3= ~83M.
While 100x10/8 is also giving 125 keep in mind that 8/10 bit encoding is used in GigEth and not in FastEth which use 4/5. The main difference is that both give extra range for special character however the 8/10 also take into account how many zero and one are send and balance them while 4/5 don't.
Never the less as mention before you don't need to worry about the encoding and frequency over the line as this is the phy responsibility and not the MAC.
Talking about Manchester there are two way to sync, one which use a pre known stream send like preamble (The problem of sync is since if you see infinite stream like ...10101010... you don't know if the source was all 0 or all 1). However in my opinion a better way to sync if you have the option to do it is to look for change. The interesting thing in Manchester is that when you get something like ....001 you have no clue about the past but you know for sure that the last 2 digit is due to 0 in the source and you are now in sync. Similar ......110 tell you the last two digits are due to 1 in the source and you are now in sync.
Have fun.