Should I have the comma after "Whitestone Army"?

Yes.

As the War of the Lance continued, Bakaris joined the dragonarmy forces in Solamnia that were battling the Whitestone Army, under the command of Laurana, now known as the Golden General.

That's a confusing sentence. Specifically. the comma that you are asking about is confusing. If the Whitestone Army is under the command of Laurana, that comma should be removed.

Thanks for your input, would this phrasing of the sentence be better?
As the War of the Lance continued, Bakaris joined the dragonarmy forces in Solamnia that were battling the Whitestone Army, (which was under the command of / which was commanded by) Laurana, now known as the Golden General.

As the War of the Lance continued, Bakaris joined the dragonarmy forces in Solamnia that were battling the Whitestone Army, (which was under the command of)(which was commanded by) Laurana, now known as the Golden General.

1) That's better.
2) I recommend that you stay with parentheses only in that sentence, rather than having them at the beginning and end and