My favorite spread with the Thoth is a one card draw. Sometimes I do a couple of one card draw's in a row, as a continuance on the theme/question, (kinda like I have a question for each "position" but I only work with one question and then I see where it leads us, like having a conversation with the deck) but usually just one card.
Like you, I found that the Thoth didn't work so well with the spreads I was used to with my RWS. Banzaf's book on the Thoth has a section on spreads which has a lot of options. The one I picked up from it and now use frequently (with any deck) is a relationship spread.
1) Person A
2) Person B
3) How Person A sees Person B
4) How Person B sees Person A
5) How Person A sees the relationship
6) How Person B sees the relationship
7) The actual relationship
It works well with any situation where you want to look at how two entities inter-relate, not just relationships. Of course this spread works very well when you apply Elemental Dignities