The phrase "to fill the layers" means to put something between different levels or sections until they are completely covered or occupied. Full definition
Top filling layer with remaining batter, making sure to scrape as much as possible out of the bowl. (84thand3rd.com)
The chocolate bars I've given you a link for say that they're 100 % cocoa, so you'll need to add more maple syrup to the chocolate filling layer. (greatfoodlifestyle.com)
The researchers believe the defect was either a hole in an otherwise filled layer of atoms or one or more interloping atoms of a lighter element such as carbon. (sciencedaily.com)