I'd say a 12cm fan in the drive bay would be great as this would bring in cool airflow from the front over the CPU and straight out the back.
leave the fan out by the PSU this will disrupt the airflow.
but the three below the M/Board could be beneficial blowing cool air inwards into the case especialy if you run a hot GPU/GPU's or are going to in the near future otherwise it may be a little overkill which by looking at you pics I think it is....but it's upto you.
Yes you can power the fan from HDD Molex fans don't use very much power really.
i agree with ^ the 120 mm fan in front will help alot as it directly cools you ram and CPU, i cant see the fan on psu but if you face the fan down ward then it can extract some of the air and cool your psu too.
as for the bottom you can leave that for a water cooling system in future if you like or you can cut it now and install a rad there later but i think its kinda pointless having 3 fans down there, max i put 2, 1 pointing to your gpu and 1 blowing to your ram.
In that case and set up a 1200 fan placed in the front as an intake will be enough, remember you can over do it with fans and have a negative result on the cooling.
80MM at top might not be bad to be a intake also,more air comming in over top to be pushed down towards cpu and such,try it both ways and monitor case temps ect and see how it goes. Looks good otherwise tho.