How to make my code 'wait' before executing rest of my code?

You can't delay for any significant amount of time. Doing so would cause your program to be terminated for running for too long.

You need to figure out a way to display your alert when it is supposed to be visible, and hide the alert otherwise. A primitive solution would look something like this (this code is completely untested)...

hidden var mLastAlertTime; // time to stop showing the alert
hidden var mNextAlertTime; // time to start showing the alert
hidden var mAlertVisible; // indicates the alert is visible

function compute(info)
{
var now = Time.now();
if (now < mNextAlertTime) {
mAlertVisible = true;

// stop showing the alert 5 seconds from now
mLastAlertTime = now.add(Gregorian.duration({ :seconds => 5 });

// start showing the alert again 20 minutes from now
mNextAlertTime = now.add(Gregorian.duration({ :minutes => 20 });
}
else if (mLastAlertTime < now) {
mAlertVisible = false;
}

// any other stuff you need to do here...
}

function onUpdate(dc) {

// do all of your drawing...

if (mAlertVisible) {
// draw the alert
}

}


if((System.getTimer() % (20*60*1000)) < (5*1000)){
// 5 second code
}
// optional
else {
// other code
}

This is beautiful. Thank you! <3
Travis thanks as well :)