When should you use the #cis//trans# as opposed to #"(Z)-"//"(E)-"# isomer naming scheme and vice versa?

The cis classification does not come with an implication of group priorities, whereas the Z classification does.

For instance, when describing the following molecules, it is OK to use cis because they are simple and have no complicated group priorities:

Here you would say cis-ethene and cis-dibromoethene, respectively.

But some molecules are more appropriately labeled Z, given that they are too complicated for cis to give sufficient information:

For the first one, you could call it (Z)-1-chloro-1-isopropyl-2-methylethene. It is still a cis/trans isomer, but Z gives you a clearer IUPAC naming. It tells you that chlorine is the highest priority, as it is the only group cis to a non-hydrogen group, yet the group next to the hydrogen is NOT a hydrogen, but isopropyl. In a case like this, chlorine is highest priority based on having the highest atomic number.

(If you interchange the methyl and hydrogen, you should get (E)-1-chloro-1-isopropyl-2-methylethene.)

For the second one, bromine is highest priority, followed by chlorine, then methyl, then hydrogen, so we call this (Z)-2-bromo-1-chloro-1-methylethene.

(If you interchange bromine and hydrogen, you should get (E)-2-bromo-1-chloro-1-methylethene.)