You pass vtcombo a combination of flags that you would normally pass to the individual components (vtgate, vtctld, vttablet). For example:
vtcombo -logtostderr=true -proto_topo "$(cat ./topology)" -schema_dir ./vschema -mysql_server_port 15306 -mysql_server_bind_address 0.0.0.0 -mysql_auth_server_impl none -db_socket /tmp/mysql.sock -db_host localhost -mycnf-file /etc/mysql/my.cnf -db_app_user root -db_allprivs_user root -db_appdebug_user root -db_dba_user root -db_repl_user root -dbddl_plugin vttest -port 15000 -grpc_port 15001 -service_map 'grpc-vtgateservice,grpc-vtctl,grpc-vtctld' -db_charset utf8mb4 -vschema_ddl_authorized_users='%'
keyspaces {