You have to buy them from a pharmacist, though you simply ask for them and they give them to you. They aren't, however, out on shelves with the cold meds. Also, they aren't sold under the same trade names here, so you are going to have to ask for them by chemical name. Claritin, for example, is sold generically. Its chemical name is Loratadine. If you write that on a paper and hand it to any local pharmacist, s/he will hook you up immediately (and cheaply, too). Allegra (Fexofenadine), over the counter in the west, is a controlled substance in Taiwan and is only available through specialist doctors in hospitals.
Price-wise, the Loratadine is roughly 100nt (about 3 USD and change) for a dozen tablets. Allegra, if you go to a hospital that offers it and have NHI, is about a biweekly supply for 150nt.
So, best advice is, if there are specific brands that are effective for you, make a note of their chemical names before coming here. Also, watch and compare the dosage. Sometimes, it's much lower. The local doc gave me 60mg tablets of fexofenadine, when 120mg are sold OTC in my home country. Sometimes, they are a bit wussy here with that sort of thing. Perhaps locals are more sensitive to these kinds of meds. But make a note of your current dosage, and take the appropriate number of pills here to reach it.
I'm the toast with the most.