It can be confusing to rely upon stage directions printed in the edition of any Shakespeare play you are reading -- The Arden, The Folger, Penguin, etc. The editors of these editions choose what stage directions to include in their version of each script, and so it is hard to rely upon one single edition for the "real" stage directions.
The place, however, that you can look in a Shakespeare play for stage directions is the text itself. Shakespeare relied upon embedded stage directions, which means that the stage directions are implied in what characters are saying. Let's look at the embedded directions in each of the scenes you mention.
Act II, scene i:
The scene begins with a sort of anti-stage direction, Banquo and Fleance commenting on the fact that there has been no striking of the hour. To mention something that the audience doesn't hear might seem odd, but it could also imply that Shakespeare intends a deathly stillness on stage at the opening of the scene.
We know the exact moment of Macbeth's entrance into the scene (and that there must be some noise that precedes him) by Banquo's "Who's there?" Shakespeare's theatre didn't, as far as we know, have directors, but lines like this one were a useful way for Shakespeare to "direct" the play from the page.
"Is this a dagger which I see before me?" This is a real question, and we have no way of knowing if there was some special effect here, making a dagger visible to the actor playing Macbeth and the audience. It is entirely possible, but, when staging the play, this question must be considered in choosing whether to materialize a dagger or not.
At the end of this scene, Macbeth mentions "The bell invites me." which refers to the command he has given a servant earlier in the scene, "bid thy mistress...strike upon the bell." So, there is a sound effect called for here.
Act II, scene ii:
This is a scene of much tension and some confusion, so there are mentions by Lady Macbeth and Macbeth of sounds and noises that both may or may not hear. Shakespeare lets the audience know this when Macbeth enters asking, "Who's there?" "Didst thou hear a noise?" and "Didst not you speak?" Whether these are actual sounds the audience can hear seems to be, like the dagger in the scene before, up for discussion.
However, before Macbeth's entrance, Lady Macbeth mentions hearing "the owl" and "the grooms...snores."
Macbeth refers to the knocking that enters the scene and continues with "Whence is that knocking?"
There is also reference to the hands of first Macbeth and then Lady Macbeth. Macbeth says, "What hands are here?" and mentions how red they are. Lady Macbeth returns with, what must also be red hands. She says, "My hands are of your colour."
The knocking escalates (referred to by both Lady Macbeth and Macbeth), adding urgency to the a very tightly wound and intense scene.
This is an interesting couple of scenes in Macbeth, because most of the real action takes place offstage (i.e., the murders are offstage and the guilt is shown onstage). On stage, we see darkness and we hear strange knockings and noises. These, of course, set the scene for the events of Duncan's murder and the subsequent aftershocks of committing such a dishonorable and heinous deed. The explicit stage directions call for a few entrances and exits, a few light cues, but mostly they are sound cues. When the text says knocking, there is a subsequent moment of being startled or scared by the characters. The Macbeths are committing actions which cause them to see and hear guilt in every sound. A noise happens, and Macbeth starts as if afraid of being caught or seen in his bloody guilt.
Implicit in the stage directions, it seems to me, are even more sounds. We know there are people talking in their sleep; we know there is the sound of footsteps as the two of them, at least, come and go; and we know there must be other nocturnal sounds associated with a night out of the ordinary. These contribute to the overall atmosphere both of the unnatural nature of this murder (for to kill a king was a guarantee of eternal damnation) and the guilt of the murderers. The simple stage direction Knocking within can be taken and used to create all kinds of suspenseful and intense moments in these already suspenseful and intense scenes.