Is there a way to write programming to make the Arduino see the D first and then the rest of the data and say hey, He said D, so down. or possibly D123 where down by a value of 123?
Yes, why wouldn't there be ?
Picking out single characters when the program knows what to expect (U or D for instance) is easy. Keep reading until you find something that matches what you expect. Then either read a fixed number of bytes which hold the number or read until an 'end of message' marker, such as Carriage Return or Linefeed is found and extract the number from the bytes read. There are even functions such as Serial.parseInt() which make it easier.