Firstly, so far as the calculator goes, you put in the housing costs you pay directly and also put in any other income, whether that's maintenance, salary or whatever. So if, for example he pays £1k per month and out of that you state your full rent of, say, £900 but also say that you're getting £100 interim maintenance.
If he pays his share of the rent direct and doesn't give you anything else, then you just put your smallish percentage of rent in as your housing costs.
So far as the divorce is concerned, if you've effectively been separated for almost two years anyway, there's probably not much point in NOT going ahead and issuing a petition. Only if you think you may reconcile should you delay any further.
If you're sure you don't want to divorce just yet, the two of you could sign a separation deed which is legally binding to a degree but could in certain circs. be overturned by the court (eg if only one of you had legal advice and it was patently unfair). Sorry have to go, will check again tomorrow.