Modern evolutionary theory doesn't really claim that one organism evolved from another in a linear fashion. What is really claimed is that certain species share common ancestors. So, going off your example, modern fish and modern amphibians likely had an ancestor in common, and then their linages branched apart and came down to modern day. Along the way, other branchings also occurred. For example, amphibians and mammals share a more recent common ancestor than fishes and amphibians.