I was originally required to notify immigration of my address on 14th April. However I went to Australia for 6 weeks returning on the 3rd. of April. Do i have to notify them 90 days after the 3rd. of April or am I still expected to notify on the 14th of April ( a little late now!)

It is 90 days, the 1st day counts as day 1, after arrival back to Thailand. In other words the clock gets reset once you leave Thailand and re-enter.

The requirement is to notify them after 90 days continuously spent in the Kingdom.

So it would be in July.

You only have to make reports if you are in the country for 90 days.

Your next report will be due 90 days from the 3rd of April including the 3rd in the count.