"Those books were not here yesterday."
Translation:Ty knihy tady včera nebyly.
In this sentence, you can use safely both of them.
"Tu" can sound a bit archaic in some sentences and on rare occasions it means "at that moment", so I recommend to use primarily "tady".
It is a strange word order. If you really need to strongly stress včera as opposed to some other day, use Ty knihy tady nebyly včera..