I would make all the new fans pull air into the case if you're using the stock Intel HSF since its fan pulls air down toward the board. That would leave you with the front and side fans as intake. The back and top fans would be the exhaust.
Yes, the fans that come with the case are both exhaust fans. They actually do a pretty good job of pulling air through the case. The last build that I used an Antec 300 on had a fairly highly overclocked E5200 and a GPU with passive cooling. I didn't need to add any additional fans. I just used the two included fans and it cooled everything just fine even with the fans set to low speed.