There are a few ways that you can specify which of carrier accounts should be charged for a shipping label.
To adjust this for a single order, your best bet is to view the full Order Detail screen and specify a "Shipping Account" in the dropdown in the Other Shipping Options section.
Once you've found the "Shipping Account" dropdown menu, select the account that you want to charge the shipping fees to.
If you need to switch carrier accounts on multiple orders at once, a bulk action is a very convenient way to do apply the account to a group of orders, assuming they already have their shipping service assigned.
First, select the orders you want to update.
Once selected, click Other Actions above your orders grid, and then select Apply Bulk Action from the dropdown menu.
From the popup, click Charge Shipping to My Account... and select the account that will be charged.
Click Confirm and the orders will update!
Additionally, this bulk action is available via Automation Rules so that you can adjust certain orders as they import into ShipStation.
Head to your Account Settings (the wrench icon in the upper right).
Next, select Automation and then Automation Rules from the sidebar on the left.
In order for this automation rule to work correctly, you will need to first have the shipping service applied upon import. So either use product defaults, service mappings, or a previous automation rule or rule action (keep in mind, automation rules apply starting with the rule at the top of the list and then work down the list from there).
If applicable, add criteria or filters that would trigger this automation rule. Then from the actions dropdown, select Charge Shipping to My Account... and choose the account that will be charged.
Click Save Rule, and ShipStation will adjust applicable new orders as they import!