This is one area of Japanese study that I hate most. It's such a hassle to remember both of the forms.
tadoushi usually is used with wo and jidoushi with ga. You can sometimes easily see that this is a jidoushi or tadoushi by looking at the word. tadoushi tend to end with eru and jidoushi with aru. Of course, there's quite a number of exceptions like dasu (out) which is tadoushi and deru which is jidoushi. Another way to recognise a jidoushi and tadoushi is whether it's used with arimasu or imasu.
hana ha narabete arimasu (tadoushi)
hana ha narande imasu (jidoushi)
I'm still not good in this area. Moshi machigattara, naoshite kudasai.