If you're sending pairs of ints, or any number of bytes, it seems you may want to consider a simple serial protocol. There are a few questions here specifically about serial command protocols for embedded systems, for example: 
- How do you design a serial command protocol for an embedded system?
 
- Simple serial point-to-point communication protocol
 
One suggestion is starting off your message with a header byte, usually something outside of your data range if possible (>90 in your case?). The following code has not been tested; it's just an idea, but it should run.
int lookingForHeader = 1;
int lookingForByteOne = 0;
int lookingForByteTwo = 0;
while (myPort.available() > 0) {
    while (lookingForHeader == 1) {
        int header = myPort.read();
        if (header == HEADER_BYTE) {
            lookingForHeader = 0;
            lookingForByteOne = 1;
        }
        // Consider incrementing a counter here and timing out if it gets too large.
    }
    if (lookingForByteOne == 1) {
        int byteOne = myPort.read();
        // Check if byteOne is between 0 and 90.
        lookingForByteOne = 0;
        lookingForByteTwo = 1;
    }
    if (lookingForByteTwo == 1) {
        int byteTwo = myPort.read();
        // Check if byteTwo is between 0 and 90.
        lookingforByteTwo = 0;
        lookingForHeader = 1;
        // Perhaps do a serial.write() here to acknowledge that 
        // a header and two bytes have been received.
        // Finally, do stuff with byteOne and byteTwo.
    }
}
Another option would be to acknowledge the receipt of each byte (i.e. receive header, respond with a special "ack header" byte, receive next byte, respond with "ack byte one", etc.). This is slower but it may fine for you.
Finally, a couple key points from the questions I linked to above:
Consider sending a checksum (i.e. sum of bytes) at the end of the message. The Arduino would add up the header, byte 1 and byte 2. If it doesn't match the check sum, then it could respond with a failure, or send again message.
Rex's answer to question [2] sums up what a message protocol might look like:
// total packet length minus flags len+4
U8 sflag;         //0x7e start of packet end of packet flag from HDLC
U8 cmd;           //tells the other side what to do.
U8 len;           // payload length
U8 payload[len];  // could be zero len
U16 crc;
U8 eflag;         //end of frame flag