Play the game as you would normally do.
If you have enough rubies, choose the "Buy Quick Ascension" http://imageshack.com/a/img538/7605/85XSzY.jpg
The further you go in levels, the more Hero Souls you will get! http://imageshack.com/a/img537/659/k9S3IX.jpg

If you are ready, click on the wrench (options) and click SAVE http://imagizer.imageshack.us/a/img633/5475/iMmvKK.jpg
Lets go than to the website http://s3-us-west-2.amazonaws.com/clickerheroes/ancientssoul.html
or check https://www.reddit.com/r/ClickerHeroes/wiki/calculators for a more compatible list of the newest version. Use ctrl + v to paste our save game data into the field under the text "Paste save data (click wrench, click Save, close the save prompt because its already copied to clipboard)"

Click than on "Import"
If you have resetted and you are back at Lvl 1, make sure you untick "Include souls gained after ascension" and click than on "Update"

On the right you'll see all your Ancients listed. Where it says, under the column "Target" like seen in http://imageshack.com/a/img673/6431/hCn4xv.png

We than go back to our game and based on that "Target information, we buy the correct Ancient upgrade the same as it is shown in the Ancient Calculator for the best benefit!!

So in my example http://imageshack.com/a/img673/6431/hCn4xv.png I need to buy 1 upgrade for Atman, 5 upgrades for Libertas, 2 upgrades for Mammon and 5 upgrades to Siyalatas. If you have Ancients and the calculator doesn't say a number, than don't buy upgrades for it as it will decrease the maximum benefit of your Hero Souls and your Ancients!

Than and only than we can proceed back with the game.
Everything will go a little faster because of these upgrades we did on our Ancients.
Don't pay attention to "New Ancient Suggestion" as it's not paying attention if you are playing the game active or idling!!

Hope this guide helps you to get the maximum out of your Ancients.