After going back and forth with Multicharts support, this is what they said.

"It appears that Kraken takes a commission from the trade, but only after it is executed

In your case regarding the portfolio, in order to calculate commission the same as Kraken, you need first spend 1% of the capital, and then calculate the commission.

There is no option to set up such a commission rule in MultiCharts, I’m afraid."

Lets say I am trying to place a trade with 1% of my account and lets say Kraken is charging .35% of the trade amount as commission. What should happen is that they take .35% of the 1%.

What is happening with the current percentage based commission rule is that Multicharts is placing trades of .65% instead of 1%. When it takes a trade and I check the portfolio/balance section of the exchange, it says that I have 99.35% in BTC and .65% in X, instead of 99% in BTC and 1%(.9965%) in X.

Although my post is about Kraken, ALL cryptocurrency exchanges take a percentage of the amount traded as commission and they do so after the trade has been executed. The current percentage based commission rule is not compatible with any cryptocurrency exchanges and it is a must that Multicharts implements a commission rule that is compatible.