A common practice is to pass authentication information in the SOAP headers. With SOAP::Lite, you can do this by creating SOAP::Header objects (just like SOAP::Data, but they'll be placed in the header):

my $headers = SOAP::Header
                  ->name( 'LoginCredentials' )
                  ->value( [                                 
                             SOAP::Header
                                 ->name('Username')
                                 ->value( $username )
                             ,
                             SOAP::Header
                                 ->name('Password')
                                 ->value( $password )
                             ,
                           ]
                         ) 
                    )
;
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The login credentials can then be passed along with any other arguments into whatever SOAP method is being called, and dealt with seperately.