From what romainl only linked to (the relevant parts of links should be quoted when answering):

You can tell syntastic which checkers to run for a given filetype by setting a variable ’g:syntastic__checkers’ to a list of checkers, e.g.
let g:syntastic_php_checkers = [”php”, ”phpcs”, ”phpmd”]

As for your question about invocation: according to the FAQ, the ”command line is constructed using an internal function named makeprgBuild(), which provides a number of options that allow you to customise every part of the command that gets run. You can set these options using global variables”. (See this answer.)