The instructions were given through the front panel switches of these computers, directly to the CPU
although 'front panel' may be too narrow - I used a device once, where I had to set the 8 switches for the 8 bits of the next command, and then press a button to put them into the memory. As for what makes those 8 bits mean something like 'add CPU register A and CPU register B', that was hard-coded in the CPU at hardware level.
To elaborate, this is called microcode. They are actually stored in *a special area of Read-Only-Memory known as the control store, local to the CPU for quick access. The instructions are essentially sequences of different synchronized electrical pulses and switches.