Your question is a little under explained.
I have coded a push pull smps in software, using 2 fets, to prevent shoot through and generate a dead band I just coded the software to turn both transistors off before chaging state, and then used a nop or 2 to give them time to actually turn off.
Ie:
01 one trans on
00 both off
nop
nop wait a little
10 other trans on
nop
nop
repeat over
I dont know atmel, however if its a 16 bit there could well be a built in pwm system, like on some of the higher spec pics, in which case if you consult the datasheet for that chip there might be a register that sets the deadtime when using the pwm module.
If your fets are under control of just your code then my suggestion would be a start.