This works so I want to write it down:

#include <SoftwareSerial.h>
SoftwareSerial xbee_serial(2, 3); 
#include <string.h> // we'll need this for subString
#define MAX_STRING_LEN 20 // like 3 lines above, change as needed. 

int in_LED = 10;
int out_LED = 11;

int input = 2;

int sendval;


//serial stuff
const char EOPmarker = '.';  //This is the end of packet marker
char serialbuf[32]; //This gives the incoming serial some room. Change it if you want a longer incoming.

void setup(){
  pinMode(in_LED, OUTPUT);
  pinMode(out_LED, OUTPUT);
  pinMode(input, INPUT);
  
  Serial.begin(9600);
  xbee_serial.begin(9600);
  
  xbee_serial.print("0,0,0.");
}

void loop(){
  if (xbee_serial.available() > 0) { 
    static int bufpos = 0;
    char inchar = xbee_serial.read();
      if (inchar != EOPmarker) { 
        serialbuf[bufpos] = inchar; 
        bufpos++; 
      }
      else {
        serialbuf[bufpos] = 0; //restart the buff
        bufpos = 0; //restart the position of the buff

        Serial.println(atoi(subStr(serialbuf, "," , 1)));
        analogWrite(in_LED, atoi(subStr(serialbuf, "," , 1)));
        
         sendval = map(analogRead(input), 0, 1023, 0, 255);
         xbee_serial.print(sendval); // Value that it sends over the serial
         xbee_serial.print(",");
         xbee_serial.print("100"); //This second byte is for the purpose of the program, it is not being used. 
         xbee_serial.print("."); //EOP marker
         analogWrite(out_LED , sendval);
        
    }
  }
  
  delay(10);
}

char* subStr (char* input_string, char *separator, int segment_number) {
 char *act, *sub, *ptr;
 static char copy[MAX_STRING_LEN];
 int i;
 
 strcpy(copy, input_string);
 
for (i = 1, act = copy; i <= segment_number; i++, act = NULL) {
 
 sub = strtok_r(act, separator, &ptr);
 if (sub == NULL) break;
 }
 return sub;
}