I agree mostly with geofelt above, but will add thoughts.
Both your proposals are poor for one particular reason. What goes in must come out. So you really should have close to a balance of air intake and air exhaust fans, which your drawings do not. Beyond that, many suggest (as do I) that the near-balance should be biased to have slightly more intake than exhaust, AND that includes using dust filters on all the intakes. All cases have air leakage points. With a small excess of intake (also termed "positive pressure", although the pressure involved is really minimal), you ensure that the direction of air leakage is from inside to out, thus preventing dusty outside air from entering at the leak points.
Doing this gets a little tricky because fan air flow ratings are given for unimpeded fans. However, the rads on a AIO cooler system, and the dust filters in front of the rad/fan assembly, both reduce the fans' airflow from the specs. So if you try to design net small imbalance based solely on number of fans, or even on calculated air flow from the specs, you can't get the right answer because the filtered intakes actually do not deliver the rated flows. As a first stab at dealing with this, you can try to use one LESS exhaust fan. So in your case, three intakes on a front AIO rad with dust filters in front of the rad, and only two (or maybe three) exhaust fans top and rear. Better yet, mount the rad at the top as an exhaust fan system with no dust filters, and place three intake fans with no rad but with dust filters at the front. Maybe the rad fans' capacity is reduced by the rads more than the impact of the dust filters on the front intake fans, getting you close to balance even though you'd have four exhaust to three intake. FURTHER, in this last option, IF you can mount at the front larger fans (say, 140 mm instead of 120) that have more air flow capacity ratings, you can get even better net flow balance.
As far as air temperatures go, many advise putting the rad at the front as intake so that the air going though the rad is room air. That is cooler than air from inside the case, which would be the situation for a top-mounted rad as exhaust. The counter-argument is that a front intake rad pre-heats the air entering the case for case cooling, even though it may be better for CPU cooling. I believe BOTH of those arguments ignores the fact that the actual operating temperature of an AIO rad (and hence the actual temperature rise of the air passing though the rad) is REALLY small - a degree or two at most - and has very little impact on ability to do the rad's job or to cool the case. This is especially the case when you have lots of fans (you plan six or seven) working to cool your system. So I would ignore those two concerns about which is the best place to locate the rad.
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