Flurry basically gives you Two-Weapon Fighting, ITWF, and GTWF at the appointed levels, along with counting your Monk Levels as your BAB when you do so.
If you're Monk 4, Fighter 3, when you Flurry, you're attack at +5/+5/+0, because your BAB is treated as +7/+2, and your Flurry is providing you with effectively TWF.
The weirdness comes into play when you get into the oddity that Flurry lets you wield weapons two-handedly, and yet still make all the attacks; that's actually 100% legal - Flurry basically gives you additional attacks at prescribed levels.
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Basically, it works like this:
A Flurry of Blows is a Full-Round Attack Action.
Flurry doesn't stack with Two-Weapon Fighting.
When you Flurry, treat your Monk Levels as your BAB, period.
At Monk level 1, when you Flurry, you gain an additional Attack at your highest Base Attack Bonus, and take a -2 Penalty to each Attack you make during the Flurry, as though you had Two-Weapon fighting.
At Monk level 8, when you Flurry, you gain a second additional Attack at your highest Base Attack Bonus Minus 5, as though you had Improved Two-Weapon Fighting.
At Monk level 15, when you Flurry, you gain a third additional Attack at your higest Base Attack Bonus Minus 10, as though you had Greater Two-Weapon Fighting.
Flurry of Blows stacks with Haste and other Haste-like Effects which give an Extra Attack at your highest Base Attack Bonus (however, Haste, Speed, Divine Power, etc. do not stack with one another - you can gain only one Extra Attack in such a way).
When making a Flurry of Blows, you may spend 1 Ki Point to make 1 Extra Attack at your highest Base Attack Bonus - this effect DOES Stack with Haste and Haste-like Effects; you can't spend more than 1 Ki Point this way, and may only gain 1 Additional Attack this way.