If you are running the subs parallel (Both on the same channel of the amp) then its perfectly normal to put them both into the same chamber. If you are running the subs off of separate channels, I would put them in their own enclosures. There are some people who would say that there's nothing wrong with putting them in the same box with different amp channels, but personally I would say you're better off dividing them.
By reflex holes, I assume that you're talking about ports. Ports require much larger airspace inside of the enclosure than sealed boxes. So you should look at the specs for the particular subs that you bought and figure out how much airspace you have in your box. Compare that with the specs for the driver and see what your best option is. In general terms, you can't just throw a hole in a sealed box and get a good ported enclosure.. It has to be planned out..