As I discovered on my last trip, it can be a bit inconvenient to cash t-cheques: most banks require your passport and you have to wait in line and go through all the documentary formalities. The government-required fee per t-cheque is 30 baht. If you're cashing five $100 Amex t-cheques, that's 150 baht, same as the ATM fee. If you can get your bank or Amex outlet to give you t-cheques in $500 denominations, that'd save 120 baht per $500.
Some Thai ATM's will dispense as much as 20,000 baht in one shot, provided your bank will permit a withdrawal in such a large amount (about $660). The most I've been able to withdraw in one transaction is 10,000 baht (about $330 these days). With the fee imposed, that works out to about 50 baht in fees per $100, or 20 baht (66 cents) more than the hundred-dollar-denomination t-cheque route. I've decided that's not worth the cheque-cashing hassle for me most of the time.
I'm leaving out of this comparison variations between the exchange rates for ATM withdrawals and t-cheques and any fees you may have to pay to purchase the t-cheques (my bank doesn't charge for them, but also doesn't have the $500 denominations). Cashing t-cheques, most Thai banks give you about a 1% haircut off the interbank exchange rate. My American bank basically gives me the interbank rate, then imposes a lovely 3% fee. So I am losing about another 2% by going the ATM route over t-cheques. If I factored that in (I usually ignore it), it might make a difference. But enough of one? Ehh.
The bottom line, then, is either get a friendly bank like Schwab or e-trade that will refund the Thai fee, or just do your exchange transactions in large enough sums to reduce the bite that the fees take: $500-denomination t-cheques, 20,000-baht ATM withdrawals, and 10,000-baht ATM withdrawals are probably the best.
For me, I'm going with the 10,000-baht ATM withdrawals, except when I'm planning on especially large outlays of cash, such as to a tailor. In those instances, I'll try and get the big t-cheques.