best way to process data received via XBEE?

ok so if i got your right, the serial buffer has every data comming from processing without any space in between.

Technically, it is "without any delimiter in between". The delimiter can be a space, a comma, a carriage return, or any other non-digit character that you want to use.

so i need to find a solution, using functions like serial.ReadBytesUntil() or anything else.

You need to find a solution. It does not need to involve a blocking method like readBytesUntil().

It could be code like below that reads and stores data, starting when a start marker (<) arrives, and triggering the use of the data only when the end marker (>) arrives:

#define SOP '<'
#define EOP '>'

bool started = false;
bool ended = false;

char inData[80];
byte index;

void setup()
{
   Serial.begin(57600);
   // Other stuff...
}

void loop()
{
  // Read all serial data available, as fast as possible
  while(Serial.available() > 0)
  {
    char inChar = Serial.read();
    if(inChar == SOP)
    {
       index = 0;
       inData[index] = '\0';
       started = true;
       ended = false;
    }
    else if(inChar == EOP)
    {
       ended = true;
       break;
    }
    else
    {
      if(index < 79)
      {
        inData[index] = inChar;
        index++;
        inData[index] = '\0';
      }
    }
  }

  // We are here either because all pending serial
  // data has been read OR because an end of
  // packet marker arrived. Which is it?
  if(started && ended)
  {
    // The end of packet marker arrived. Process the packet

    // Reset for the next packet
    started = false;
    ended = false;
    index = 0;
    inData[index] = '\0';
  }
}

Where it says "Process the packet", you could use strtok() and atoi() to do the processing, if you use a delimiter between the values that is different from the delimiter(s) between the packets.

The first idea i come with is:
i set a little Timeout on the arduino serial side, so that it does not search in the buffer for too long

Not necessary, as you can see above.

on the arduino serial again, i use serial.ReadBytesUntil(character, buffer, length) (character to find, length will be "3" as i want integer like 100,999, am i right? ; still don't see how i have to declare the "buffer" )

Length will not be "3". It might me 3. Huge difference. You'd declare buffer just like declared inData above.

Comments can go before a block of code. It is not necessary to tell a story next to the code. In fact it is annoying to try to follow code AND comments that way. If a story is necessary, and I'm not arguing that you shouldn't tell a story (even if it is only to yourself), put it before the code.