When I use the Mega 2560 additional serial ports, I realize that it is active low, active high. I know that TTL is active high and the serial port is obviously stated in arduino serial port page. I also found out that the receive pin flashed (put an LED) when I typed in to the serial monitor. Is this a mistake or problem?
The Serial Class of the Arduino uses Typical usage of the Serial Ports is the USART in Async mode. Which is hard coded to IDLE state of HIGH or 1 or VCC.
http://midas.psi.ch/mscb/hardware/bits.gif (picture wont add - so here is a link to it)
If you need to drive the TTL inverted from its traditional values, the Serial Class can not do this. However, you can use the SoftwareSerial Class and enable the inversion in the constructor
SoftwareSerial(uint8_t receivePin, uint8_t transmitPin, bool inverse_logic = false);
As for why would someone want to invert the TTL UART. In some cases it is possible to drive RS232 directly. As RS232 converters inverts the TTL to +12V/-12V. 5V = -12V and 0V = +12V. So depending upon the RS232 receiver, it may actually trip its TTL output at 2.5V and not 0V. If so then using the SoftwareSerial Class with inverse logic may drive the RS232 input of another device, without requiring a RS232 transmitter on the Arduino's TXout pin.