The switched nature of Slots 3 & 4 are only a problem when both slots are being used simultaneously.
As per your situation, lane configuration is more of the issue when just looking at the specifications (8x lane card stuffed in a 4x lane slot). So moving it to Slot 2 (16x lanes) would make better sense by that logic (doesn't take into account real world conditions though). This basic logic actually holds true for most cases (i.e. if you were running an ATTO or Areca, and using sufficient drive counts;
n >= say 5 SSD's or 12 mechanical HDD's).
Realities to consider for your card:
- There's been mention that it will only work in Slot 3 or 4 due to the SATA port data connections over PCIe traces in the 2009/10 systems.
- The card isn't fast enough to saturate the 4x lane slot anyway (it's a slow card for what you get - the price/performance ratio is horrible). 4 ports is the biggest limitation here, and it doesn't work with SSD's according to Apple (ignoring the rest of the card, such as the processor used).
So I'd put the time in to read the manual that came with your card to verify #1, and check your throughput data to check #2 (worst case, in an '06 - '08 system, Slots 3 & 4 are Gen 1.0 = 250MB/s per lane, so the slot is capable of 1GB/s, double that in '09/10 systems). Not sure of the card's specification in terms of lane spec (Gen. 1.0 or 2.0), but it's just not fast enough to matter from what I've seen anyway.
So to keep things simple, leave it where it is, and leave Slot 3 empty.