There are two meanings for "after all" in English as an idiom. One (meaning 2 in Wiktionary) almost always goes at the end of the sentence and means "contrary to expectations" or "however". For example:
We thought my parents would visit us over the holidays, but there was a snow storm and they couldn't come after all.
In German you can just insert doch with the same effect:
Wir dachten, meine Eltern würden uns über die Feiertage zu besuchen, aber es gab einen Schneesturm und sie konnten doch nicht herkommen.
I think what you're talking about is the other meaning (1 in Wiktionary) of "after all", but this doesn't have to be used with a quotation and it can go before, in, or after the phrase it's referring to. For example (from Wiktionary's usage example):
Of course he won't give you credit. After all, his first and last concern is his company's profit margin.
The last part could equally well be phrased "His first and last concern is, after all, his company's profit margin," or "His first and last concern is his company's profit margin, after all."
This meaning of "after all" is usually translated as Schließlich: Schließlich ist seine erste und letzte Anliegen die Gewinnmarge seines Unternehmens.
The saying Alles hat ein Ende, nur die Wurst hat zwei, means something like "Nothing lasts forever" or "All good things must come to an end," but with a pun tacked onto the end playing on the double meaning of Ende. If you were going to shorten this for a quote then I think you'd just use the first part since the pun doesn't really mean much without it. It could be used with schließlich but it's difficult to do without changing the exact wording, so perhaps Der Urlaub ist vorbei, schließlich hat alles ein Ende. You'd have the same issue with any adverb, so if you were really concerned with preserving the exact words then I would go with a looser translation and use aber: Der Urlaub ist vorbei, aber „alles hat ein Ende.” This changes the meaning slightly but I think it still works.