I once built a tunnel wide enough for two wagons to pass abreast to connect an elf-occupied island to the mainland. I started the project by building a service tunnel one z-level below for maintenance & construction and a drain system to collect water, then sent the miners to dig the main tunnel once I knew the general geology and the locations of the aquifers. Unlike most of my drains, this one actually saw use when I popped out on the far shore to build the south portal and the waves sent water trickling down.
The bulk of the fortress was at the north portal, but because of the distance I had to build a mini-fort with housing, lounges and barracks to support the workers and troops at the south portal. Food was brought from the north portal, which in the days before minecarts required a lot of hauling.
With most of my fortress below sea level and large portions beneath the ocean floor, I was more careful than usual about flood control. The tunnel access from the living areas had redundant doors and pressure-reduction diagonal passages, the service & drain tunnels could be split into sections, I had multiple cavern drains and I installed airlock doors & a food/drink stockpile in the tunnel control center to maintain operation even if it were flooded.
FPS was adequate despite the large embark size and the old computer I was using at the time. On the other hand, another oceanfront fortress with a temperate climate and a similarly-sized embark froze for an hour when the ice melted every spring. I have a much faster computer now, but I'm still leery of a large ocean embark that's not in a hot climate.