You can probably start by explaining the difference between linking verbs (be, seem, appear , become etc) and action verbs. As a non-native speaker of English I've never had this problem because it's the same in my mother tongue. If your students struggle discriminating between the two forms, I'd say they speak an entirely different language or so it seems to me.
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Paul Burnshe's confused about writing 'does it your pen' or 'is it your pen'As a sentence, "Is it your pen?" needs a question mark (as well as a capital letter). Do you intend it as a question, as a sentence by itself, or do you intend these to somehow be parts of longer sentences?