The ATSAMA5D35A-CU is a high-performance, ultra-low-power ARM Cortex-A5 processor-based microprocessor (MPH) developed by Microchip. Control panels, IoT applications, and industrial automation all make extensive use of it. When building an application circuit that uses the ATSAMA5D35A-CU, keep the following points in mind:

1. Power Supply: The ATSAMA5D35A-CU operates at different voltage levels; thus, your power supply needs to accommodate these levels. Generally, you'll require a core supply of 1.2V and I/O supplies of 3.3V and 1.8V. To cut down on noise, decoupling capacitors should be positioned close to the power pins.

2. Reset Circuit: The ATSAMA5D35A-CU has a reset pin that should be connected to a reset controller, often a simple push-button switch. An external reset circuit can also be used to reset the device in case of power supply instabilities.

3. Clock Source: The device requires a clock source for its operation. An external clock signal, an internal RC oscillator, or an external crystal are some alternatives. For high precision and stability, an external crystal is generally preferred.

4. Memory Interface: The ATSAMA5D35A-CU has a flexible memory interface that can interface with various types of memory like DDR2, LP DDR, and MLC NAND flash. The requirements of the application would determine the memory and interface strategy to use.

5. Peripherals Interface: The ATSAMA5D35A-CU has various peripherals like USB, Ethernet, SPI, PART, I2C, etc. The layout and connections should consider the requirements of these interfaces, including trace impedance, lengths, and signal integrity.

6. Boot Configuration: The device supports multiple boot modes, which are selected using the state of specific pins at reset. Consider this when designing your circuit.

7. Thermal Management: Opus generate heat during operation. You may need to consider a heat sink, especially for applications involving heavy computation or operating in a high-temperature environment.

8. Interface for Programming and Debugging: The gadget is compatible with the JTAG interface for programming and debugging. The JTAG connector should be accessible in your layout.

As always, ensure to follow the guidance from the device's data sheet and relevant application notes from Microchip while designing your circuit.