The flat file schema wizard allows you to select the codepage (encoding) of the source/target schema. If you don't find the exact one you expect, there are ways around it, fortunately. First, consider how the flat file disassembler recognizes the encoding of an incoming flat file:
http://www.winterdom.com/weblog/2005/09/08/SelectingTheEncodingUsedWhenParsingFlatFiles.aspx
Once you know that, it's easy to see how to tell it to use a given encoding to interpret an incoming file. If the usual spots don't list the encoding you want, chances are you might be able to use my FixEncoding pipeline component in the decoding stage of your receive pipeline to select a different encoding.
Finally, you need to understand how the FlatFile Assembler finds out the encoding to write the flat file into, for that, check here:
http://msdn2.microsoft.com/en-us/library/ms964120.aspx
Hope this helps!