The baud rate can be set in the constructor of the SerialPort class in java.
To set other parameters I found only the way to set it inside the jni code.
In the android-serialport-api project the is a folder jni with the c-sources that communicate with the underlying driver. There you can configure the termios structure.
E.g. you can enable parity by adding the line
cfg.c_cflag |= PARENB;
A description how to set other parameters of the termios interface can be found here:
http://en.wikibooks.org/wiki/Serial_Programming/termios
When you have made your changes inside the c code you have to compile it with the android NDK.
First download the ndk from the android web site, and start in the android-serialport-api directory the ndk-build programm. This will compile your C code and produce the libraries needed.
A description can be found here:
http://developer.android.com/sdk/ndk/index.html