You have to use the INSTALLSQLDATADIR parameter. Problem is that this will only accept one directory for data and log files.

In case you want to have separate loctions for data and log I would advise run a post install script.

For Datafiles:

EXEC master..xp_instance_regwrite N'HKEY_LOCAL_MACHINE', N'SOFTWARE\Microsoft\MSSQLServer\MSSQLServer',N'DefaultData', REG_SZ,'D:\MSSQL.1\MSSQL\DATA\'

For Logfiles:

EXEC master..xp_instance_regwrite N'HKEY_LOCAL_MACHINE', N'SOFTWARE\Microsoft\MSSQLServer\MSSQLServer',N'DefaultLog', REG_SZ,'E:\MSSQL.1\MSSQL\LOG\'