flex and bison generate C code from their respective sources (.l and .y). You have to compile them and link resulting objects with the rest of your application. At some point the application calls yyparse() (which is the entry point to the parser).
If you have more specific question, please elaborate.
At the command prompt, typing flex something.l gives you lex.yy.c file. Similarly, bison something.y generates yy.tab.c and yy.tab.h files. You may or may not write another C file with main() calling yyparse - inspect something.y for a presence of suitable main(). Assuming it is already there (and assuming gcc as a compiler), type
gcc -o executable yy.tab.c lex.yy.c
. How to integrate it into Java, I have less clue than you.
PS: of course, you need flex and bison executables.