Theories on learning with Multiple External Representations (MER) claim that low prior knowledge learners in science have difficulties using MER, which are seen as necessary to achieve a conceptual understanding. In two experiments, we analyze the mechanisms underlying the learning of chemistry with MER. Our first experiment focuses on how MER can support learning. We found no difference in learning gains of conceptual understanding, regardless of the format (whether MER were provided or not). It is concluded that chemical MER on themself cannot be seen as learning aids. The second experiment compares three types of instructional aids (prompts, prompts with an answer, and note-taking) to determine which types of aids enhance learning with MER. Contrary to the findings of Seufert (Learn Instr 13:227-237, 2003), path-analysis suggests that the lowest prior knowledge group benefits the most from instructional aids such as prompts and note-taking. These aids guide learners' attention towards one specific representational format (symbols), while other formats (submicroscopic representations) receive less attention.