I think I know want you want but not too sure. If you can paste a screenshot showing layers ?
Gimp will use the first (bottom) layer as a canvas size and subsequent layers only 'show' that size. Generally you need to open the largest layer first.
For an existing PDF where the layers (pages) are in order, make a new canvas large enough for all and then open the PDF Image -> Open as Layers
Want to add the different sizes to the (smaller) first layer. Several ways, scale the large layers down or scale the small layer up.
Gimp will use the first (bottom) layer as a canvas size and subsequent layers only 'show' that size. Generally you need to open the largest layer first.
For an existing PDF where the layers (pages) are in order, make a new canvas large enough for all and then open the PDF Image -> Open as Layers
Want to add the different sizes to the (smaller) first layer. Several ways, scale the large layers down or scale the small layer up.