No, you can't
Unfortunately, spells only do what they say they do. They have a fixed area of effect, unless they say otherwise - if they do, usually they include "up to x feet" instead of "x feet".
For example, wall of fire spell description says
You can make the wall up to 60 feet long, 20 feet high, and 1 foot thick, or a ringed wall up to 20 feet in diameter, 20 feet high, and 1 foot thick.
so you can make the wall shorter or smaller (in case ringed wall).
The darkness spell description says:
Magical darkness spreads from a point you choose within range to fill a 15-foot-radius sphere for the duration.
The description of the silence spell says:
For the duration, no sound can be created within or pass through a 20-foot-radius sphere centered on a point you choose within range.
Both don't say "up to", so you can't reduce the area of effect of the spells.
Silence area of effect won't move once cast, so your scenario casting silence around your shoes to move sneakily won't work well, because the silenced area won't stick to your shoes. Darkness however, can be cast onto an object, so you can cast darkness on an object and put it within a box, and only opens it when you need the darkness.
At most you can only position the area to exclude your allies, like targetting higher or farther etc. Remember that most spells require you to have line of sight to the center of the area of effect.