After the schematic design is complete it’s time to move to layout. In this step you are locating where each component will go on the board and routing the electrical connections. Important parameters such as board size, number of board layers, and minimum space and trace width must be determined first. In general cost increases as the number of layers increases and the minimum space and trace width decreases. For a beginner project two layer boards are inexpensive and general sufficient for simple Arduino boards.
More advanced tools have auto placement and routing that makes this process go quickly. The Eagle auto router works fairly well but I still place components manually. Given that these circuits are relatively low frequency, component placement is not extremely critical (after all a breadboard version usually works). But, for manual component placing, it’s best to keep associated components together on the board. For example, most Atmel microcontrollers can use a crystal oscillator. Placing the crystal near the associated pins on the microcontroller is good. This minimizes the number of vias and trace length required to connect the crystal to the microcontroller.
After placing and routing, perform a design rule check. At minimum, this step checks that all independent electrical signals are separated by the minimum space that can be etched on the board. Design rule files can be created or downloaded from the fabrication vendor.