Seriously, the most liberating thing I ever did in Dwarf Fortress was deciding I was going to start embarking on aquifers and keep practicing breaching them until I got it down. I would recommend those practicing download an older version where you can see how many levels of aquifer there are so you can start with easier one level ones and its probably worth learning both the 'ring/plug' method and the pump method to see which you prefer (both have pros and cons).
These days with the pump method a single layer aquifer is no problem at all and I can punch through endless levels without major hassle (beyond all the time it takes). The only special supplies you have to take (assuming there are trees on your embark) two (though its faster with four) pieces of useable stone (to make one or two pumps).
So yes, with a minimum of two stones (and access to trees on embark) you can punch through literally any aquifer, regardless of number of layers.
Its great to learn for two reasons:
1) So you don't end up in situations like the OP, where you have an otherwise perfect embark but 'arrg! an aquifer!"
2) After you get used to it you may find you like aquifers. I love them and actively seek them out, in fact I actually say "otherwise perfect embark but no aquifer, oh well keep looking". They grant you endless fresh water to any point in your base with minimal work. You can drain it to lower levels and if you are above the aquifer (using the soil layers) you can just pop a hole in and set up a well. Its great for farming (not as big a deal now that they fixed underground dirt needing irrigated before it could be used), great for getting fresh water for emergency hydration, and if the mood strikes its great for traps. They are an amazing and underutilized resource.