Blowing in is usually standard for the side fan, but as has been said in some cases it can be out.
Personally, when planning case airflow I usually try to ensure air input (in CFM) is equal to or greater than air output, and of course try to ensure the hottest components get the coolest air...
If you have dust filters on your input fans, and slightly more CFMs going in than coming out, I find that little bit of positive pressure in the case helps prevent the case from sucking in dust through other unfiltered gaps, so the only dust is that caught by the filters which are far easier to clean than your CPU/GPU sinks. Less dust in turn helps keep it running cooler for longer.
So, for example, on an Antec 300 I have: 2 front 120mm's in and one side 120mm in for a total of 3 matched 120mm fans blowing in... and the back and top 120mm blowing out, plus the 120mm in the PSU of course, for a total of 3 in and 3 out... the PSU is lower speed/CFM than the others so there's more input than output, and hence the case doesn't suck in any dust through any other non-filtered gaps.
From your description it sounds like you'll want the side fan sucking air in and blowing it across the GPU(s).... but it can depend where your heat load is. Since not all sinks on the boards have temp monitoring, one trick I do to find what needs it most is run the PC at full load for a while, then open it up and do the old "finger test"... with one hand grounding yourself on a bare metal part of the chassis to prevent ESD, put a finger of your other hand on each heat sink (obviously taking care not to touch any electrical contacts themselves) and see if you can keep it there for up to a minute before it gets too hot (obviously use common sense and take it off before letting yourself get burned, and don't stick it on a sink you know runs at 80c lol). This way you'll soon find out which heatsinks are hottest and need the most cooling. In my case it's the passive-cooled northbridge sink on my gigabyte mobo... that bitch must be running over 60c because I can't keep my finger there for more than a minute... so I added a silent 80mm fan right on top of it... and it now keeps the temp right down at 31c even under load, which should help the component live longer.
edit: oh, and of course don't go trying the finger method in PSU's or TV sets... only on stuff you know is low voltage, or you'll get a nasty suprise.
In fact if you're unsure always seek advice from someone with good electronics qualifications.
Hope some of this is useful.
