Question

fluorescent dyes help scientists see the movement of compounds and strutures in living cells

Answer 1

Indeed they do. Though in practical terms, many (not all) fluorescent dyes are deadly to cells or involve staining procedures (such as punching the cell wall full of holes to get the dye into the cells) which kill the cell anyway. So scientists have other ways - tagging molecules of interest with fluorescent proteins is the classic alternative - of doing the same thing only more efficiently. Just in general.