Yes, you can relocate the Flash API code. Here's how:
1) Make a copy of Psoc Designer\tools\cms.a
2) Rename the copy to something like fcms.a (in the tools folder)
3) Edit fcms.a (it's a text file). Change the line A text size FF flags 0 (near the top of the file) TO: A flashblockarea size FF flags 0
4) Create a file in the project folder called custom.lkp
5) Add the following line: fcms.a -bflashblockarea:0x????
6) Change the start address to your desired location.