In order to create a positive air pressure in the case, hence less dust, means having more fans blowing in than out so that the case has a net positive air pressure.
Positive air pressure alone will not promote less dust entering the case. You'll have to have good intake filters too.
Adding more intake fans will introduce more dust into the case unless you have a very good filtering system. Bottom fan will be worst offender.
(1) Since warm air naturally rises top fans should be set to help exhaust rising warm air, not fight against it's natural tendency to rise.
(2) Positive pressure is less important than "air exchange" - moving cool air in and warm air out.
CM 690 has about 1.5 cubic feet internal volume. If you're intake fans deliver 90 CFM of air though the case you're doing an "air exchange" about every second. That should be enough to keep any desktop system cool enough.
Why not test the system temps with the stock fans first. Then test after adding a top fan. Keep testing till you know how your fans are affecting the overall system temps. Try different fan configurations and measure those temps.
To be honest I'd trust the case design engineers that the stock fans are "good enough" for a even a "hot gaming system".
IMO, the one with out the window is better because you could get it a lot cheaper and has 1 additional fan spot where the window is, buts it your choice. there is not much different between the two other than that. (the front LED fan is really weak, you might want to switch that, but since you are adding more fans in anyways, i dont think you have to.)
The classic configuration is cool air into the bottom/front of the case and hot air out of the top/rear of the case. An additional fan on the side panel can be used to direct cool air toward the video card or cpu depending on location.
One way or another, directly or indirectly, dust is always going to be a problem.
There is an additional problem. Dust filters, perforated mesh, and fan guards severely restrict ventilation, airflow, and cooling.
I have a CM690. In it there is a filter for the front and bottom. The sides are the only ones that needed filters, (I used black knee highs trimmed to fit). While I was still shopping I thought I saw a filter on the windowed panel. Front bottom and side should be intake, top and rear should be output, no filters should be needed for the output if the input filters are doing their job.
I agree completely with WR2, no matter how carefully you plan, it's still possible to get "dead air" spaces where you don't want them to be i.e. at HSF and around the GPU. After installation, always check temps. After any changes you make, check temps. Even after adding a fan or 2 or 3, check temps.