1. taking everything into consideration
it's not that important in the larger/greater scheme of things
Essentially, this expression is about putting things into perspective. Something considered on its own may seem to be a big issue, but when taking everything into account, or looked at 'in the greater scheme of things,' it may appear insignificant. For that reason, the expression is often used, in both a social and professional setting, to reassure or commiserate with somebody, or to clarify a situation.