Ahoy,
yes the Beads will settle within a few minutes or less, depending on size and magnetic interaction. We strongly recommend to always shake up the beads before you take an aliquot. Especially once the beads are diluted to working strength for your respective protocol, make sure you aspirate with a pipette or shake before you take up the volume you require. The actual binding of DNA/RNA happens very rapidly and while you can shake the solution containing Beads + Sample to make sure you will have achieve maximum yield this is usually not necessary.
Feel free to ask more if I did not answer your question completely.
Cheers
Tim