The Init SystemThere is a window in Maptool that contains campaign macros. Maptool distributes these macros when a client connects so anything your players will be able to see anything you place here. The bottom part of the panel contains a macro group named Initiative. Four of these buttons are for the GM to use to run Initiative.

The DrawInitCard button deals an intiative card for each selected token. It outputs the card draws to the chat window as shown below.

The Next button advanced the initiative order. Each time Next is invoked you see a message in chat saying whose turn it is and who has yet to act.

The Red Reset button is used before (or after) you leave the combat round and revert to normal game time. It has the effect of collecting all the cards and purging any internal counters.
The Green Init Control button takes the place of the normal maptool Initiative window. Its a small yet powerful window that allows the GM to track Initiative, states, and perform trait and attack rolls. In the window below you can see the Mage has initiative and the Troll is shaken. The Next button on this window advances the init and functions the same way as the Next button on the campaign macro window. You can also delete combatants from the order by selecting the checkbox and clicking on the Delete Key. If you Toggle Hold on a combatant they will show as on hold in the chat output, an hour glass symbol will appear on the combatants token, and the combatant will not draw an Initiative card until that combatant goes off hold. 'Trait Roll' and 'Attack' will invoke a dialog window allowing the GM quickly perform these actions without leaving the Init Control window.

There are a few rules associated with going on Hold. You can't go on hold if your turn as passed. If you try you get an error. Likewise you can't go on hold between rounds. Combatants that go on hold are give a card equivilant to an Ace of Spades to indicate they go before everyone else who hasn't drawn a joker.
After the GM has stepped through all the combatants for the round, a message will appear in chat letting the players know the round is over. The Init Control panel then automatically redraws init cards for all combatants it finds on the current map that were in the last round. If you need to add new combatants then you'll need to use the DrawInitCard function on the Campaign macro window after selecting the new combatant(s).
Another handy macro button is ShowInits which displays the Init order in chat with the card symbols held by each token. You can also use the ShowHands macro to display the cards graphically in a separate window.
Now lets put it all together. In the scene below a Mage, Fighter and Elf have started a fight with a poor, innocent Troll who was just minding his own business when these so-called adventurers performed the fantasy equivalent of a home evasion.

The GM resets the Initiative deck using the Red Reset Init Deck button, selects all four tokens, and clicks on the Green DrawInitCard button in the campaign macros. The following output dumps to chat.

The so-called Hero goes first and attacks the Troll with his long sword. The player of the Hero would either roll the attack from the character sheet or use the 'Use Weapon' macro button to perform the attack. Unfortunatly for our Hero, he failed critically. HA! Serves him right for attacking a Troll.

The GM would then advance intiative from the Next button on either the Init Panel or the Campaign Macros panel. With a Queen of Spades its now time for our Troll to attack. As the GM, I'll attack from the Init Panel but I can just as easily do so from the Troll's character sheet. By marking the Troll's checkbox on the Init Panel and clicking the Attack button I get a dialog asking me which weapon I wish to use. The Troll has axes and claws to choose from but I decide to use axes.

After selecting the Axe I get the following window. This same window appears in the lower half of the Character Sheet window if you click Axe in the Troll's gear section.

The Troll does well! He manages to shake and wound the Hero. But the fight is not over yet. It is the Elf's turn. She fires her bow with the following result.

She missed! But had she hit it would have damage the Troll badly. Too bad the adventurers are all out of Bennies. But next up is the Mage. He casts a Bolt at the Troll and rolls 1 on his spell casting die and is automatically shaken.

As we end this little demonstration things are looking good for our Troll.

And no, I didn't fudge the rolls to help the Troll. So that's a brief example of how Initiative works in Savage combat within my framework. Please download the campaign file above, give it a try, and let me know what you think.
Edit: Update on the combat above. I needed to test some things for displaying events and so ran the above combat to its end. The troll managed to incapacitate the Hero and the Mage and had the Elf on the ropes. The Elf had to drop to a rapier, which increased his parry by 1. One lone pointed ear elf managed to Shake the troll allowing the elf to retreat and draw his bow again. The troll never recovered from shaken and the elf and kept getting wounds (even with regeneration ability). The elf was able to incapacitate the Troll and get his friends out of there.