The assembler features a 2x2 crafting grid and will automatically assemble items as long as it has energy, items in the input slots, and space for the finished product in the output slot.
Some machine components can be crafted without an assembler, but doing so uses significantly more resources.
The order of the components in the input slots does not matter. If a machine needs 2 of the same item, it can also take both from the same slot.
Automation
For fine-tuned item input, an inventory proxy addon can be used to control which items go where. Alternatively, the assembler also has different input modes. The "Fill-Evenly" or "Sided" variants can make automation much easier for some setups.
Automation can also be done via AE2 / RS2. Pattern providers work out of the box with the assembler.
Efficiency
Using the assembler is the recommended way to produce complex components like motors or magnetic coils. Crafting these components manually is possible but consumes more resources than using the assembler.