Estragon struggling with his boots is indeed a very important image in Beckett's play and this stems from the importance of the boot as a stage-prop as well as Beckett's emphasis on the trivial little sufferings of human beings. Beckett has always been seen as a very metaphysical writer and someone who portrays the metaphysical absurdity of the human condition but we must understand that like Chekhov, Beckett also draws our attention to the little sufferings we ignore. Consider this line from First Love, a Beckett story--"What do I know about the human destiny? I can tell you more about radishes."
Estragon's efforts to put on the boots give him pain since it is a misfit and it elicits from Vladimir, an important response where he says that man always tends to blame the other, especially the tools at his disposal for his failure or pain and never acknowledge their own folly. Folly is a favourite word of Beckett and his whole canon brings us face to face with our partial knowledge and foolish self-confidence. It has a humbling effect thus.
The boots go missing and in Act II, there is enough confusion whether it is the same pair of boots. All changes under the garb change-lessness. . Everything in the world of the play seems to have its double--even the pair of boots.
The empty space in the boot or in the hat are all very important as they symbolize the gaps in the construction of the self.
As for Beckett's stage-directions, what directions are you talking about? Those relating to the boots? Estragon seems to wonder at the empty space within the boot and thinks that there must be something inside that is giving him all the trouble.
A general answer would be please take all his stage directions very seriously. Everything is precisely worked out by Beckett. His are some of the most serious and deeply contemplated and absolutely spot-on (in terms of the intended effect) directions that you ever find in the history of Modern Theatre. You can consult the Theatrical Notebooks of Godot. They are published by Faber and Faber.