Component layout on PCB

Reading Netlist and placing footprints from components

Select Read Netlist from Upper Toolbar. Click on Read Current Netlist. Then select Close

Placing components on PCB

Click on component to select it and use the M key to move and the R key to rotate. 
Place all components on board to match in picture.

Ensure the 6 Pin connector is Vertical and placed on the right side of the board.
Ensure Pin 6 VCC  on the 6 Pin connector is at the top of the board.
Ensure Pin 1 on all the Resistors are on top and are aligned with the Pin 6 VCC on the 6 Pin connector.
Ensure Pin 1 on C1 Capacitor is aligned with Pin 1 of the Resistors.
Ensure Pin 1 on Y1 Crystal is on the top.

Connecting Traces

Reading Netlist and placing footprints from components

Select Read Netlist from Upper Toolbar. Click on Read Current Netlist. Then select Close
Adjust any component that needs to be aligned.
Click on component to select it and use the M key to move and the R key to rotate. 
Place all components on board to match in picture.

Start Routing Traces

Select Route Trace right side tool bar. Click on Pin 6 VCC and drag straight across to R2.

Place just above the wire as seen in picture below

Connecting the Clock Crystal

Select Global Label right side tool bar and type OSCO in the text field.
Rotate and connect to Pin 2 of RTC. 
Hover over label and hit C key to Copy the label and then connect the copy to Pin 2 of the Crystal.
Select Global Label and type OSC in the text field. Rotate and connect to Pin 1 of RTC. 
Hover over label and hit C key to Copy the label and then connect the copy to Pin 1 of the Crystal.
As seen in picture below

Connecting I2C SDA & SCL

Select Place Wire from right side tool bar.
Draw a wire from the Pin 4 of the 6 Pin Connector to SCL Pin 6 of the RTC 
Draw a wire from the Pin 3 of the 6 Pin Connector to SDA Pin 5 of the RTC
Draw a wire from the bottom R1 and connect to the wire running from Pin 4 to PIN 6 (SCL) of the RTC
Draw a wire from the bottom R2 and connect to the wire running from Pin 3 to PIN 5 (SDA) of the RTC
As seen in picture below

Connecting the INTA

Select Global Label right side tool bar and type INTA in the text field.
Rotate and connect to Pin 2 of the 6 Pin Connector. 
Hover over label and hit C key to Copy the label and then connect the copy to Pin 7 of the RTC.
Select and Move R3 to connect bottom between the new label INTA and Pin 7 on the RTC.
Hover over the VCC symbol and hit C key to Copy the VCC symbol and then connect the VCC symbol to the 
top of R3
As seen in Figure below.

Finishing up and adding the Ground

Select Place Symbol and then type GND in pop up search window and click on OK. 
Connect GND symbol to Pin 1 of the 6 Pin connector. 
Select Place Wire from right side tool bar.
Draw wire from Pin 1 on 6 pin connector to Pin 4 on RTC. 
Hover over the GND symbol and hit C key to Copy the GND symbol 
Select r to rotate the symbol and connect to Pin 5 of the 6 Pin connector.
Hover over the GND symbol and hit C key to Copy the GND symbol again.
Connect GND to bottom of C1 
Hover over the VCC symbol and hit C key to Copy the VCC symbol 
Connect the VCC symbol to the top of C1

---