Here's my approach to the significator. If I'm throwing a spread in reference to a question, I'll mentally choose which of the 78 cards represents the question.
The card might be one of the usual court cards, as the books stress, but I find the selection too limited. So often questions are not about some individual, but a set of circumstances. Suppose someone's asking about a home purchase, because now there's a new child. You could choose the Kind of Wands, or whatever, but a good choice might also be 10 Pentacles, or 6 Pentacles, or 4 Pentacles, since the query is about a house, money, family, security, options... The choice depends on the shading of the question and the insights you hope to gain.
Keeping that card in mind, I simply leave it in the deck, have the Questioner shuffle the cards, and throw the spread. I would check to see if that card is part of the spread or not, and read and react to the spread accordingly.
To me, it seems unhelpful to leave so important a card as the significator 'out of the running' in throwing a spread.