This can be configured in Settings -> Buying. The "Currency" option is the main currency type and the "Decimal Currency Type" option is the decimal value for this currency.
If you want the decimal value of Exalted Orbs to be Chaos Orbs, you would select Currency: Exalted Orb, Decimal Currency Type: Chaos Orb.
If you want the decimal value of Chaos Orbs to be Orb of Alchemy, you would select Currency: Chaos Orb, Decimal Currency Type: Orb of Alchemy.
With these settings:
An item costing 1.5 Exalted Orbs will use 1 Exalted Orb, and the value of 0.5 Exalted Orbs as Chaos Orbs.
An item costing 1.5 Chaos Orbs will use 1 Chaos Orb, and the value of 0.5 Chaos Orbs as Orbs of Alchemy.
If 1 Exalt = 100 Chaos Orb, and the item cost is 1.5 Exalted Orbs, the bot will look for 1 Exalted Orb and 50 Chaos Orbs.
If 1 Chaos Orb = 4 Orb of Alchemy, and the item cost is 0.5 Chaos Orb, the bot will look for 2 Orbs of Alchemy.