Elementary students' early development of embedding and disembedding is complex and paves the way for later STEM learning. The purpose of this study was to clarify the factors that support students' embedding (i.e., overlapping shapes to form a new shape) and disembedding (i.e., identifying discrete shapes within another shape) through the use of filled shapes as opposed to shape frames. We recruited 26 Grade 1 students (~6-7 years old) and 23 Grade 3 students (~8-9 years old), asked them to work on two layered puzzle designs from the Color Code puzzle game, and interviewed them about their thinking processes. The first graders had higher success rates at fixing and embedding the tiles correctly, and students at both grade levels improved on the three-tile design when encountering it a second time about two months later. The four-tile design was more difficult, but students improved if they could identify a correct sub-structure of the design. Successful students used a combination of pictorial shape strategies and schematic location strategies, systematically testing tiles and checking how they could be embedded. The results suggest that helping students focus on sub-structures can promote their effective embedding.