I am using the first method, because most sims i fly are about vintage planes, which had a centered stick. I have built a center console for my stick and a second console, which is a bit smaller for my throttle. Stick and throttle are secured with velcro. Works like a charm.
I used to play in a sidestick setup back in the old X-Wing and Falcon days.

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Intel Core 2 Quad Q9450, 4x 2.66 GHz, 12 MB L2 Cache Total, 1.333 MHz FSB, 45 nm (@ 3.42 Ghz)
ASUS P5QC motherboard, Intel P45 chipset, FSB 1.600 MHz
ASUS Silent Knight II CPU Cooler
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TOSHIBA RV555D 37" LCD, 100 Hz, Full HD
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Sound Blaster X-Fi Fatality Gamer
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ANTEC EarthWatts 750W PSU
TrackIR3 Pro
HOTAS Cougar with "Uber NxT" gimbal mod
SIMPED F-16 pedals