When you set the configuration for a new aircraft there are as many different processes as there are manufacturers. The terms of the contracts for all major equipment selections - engines especially - will depend partly on the negotiator and partly on the operator's bargaining strength. Big Airways will get a better deal than Little Airways, its just common sense.
On most airliners you have a choice of engines and you negotiate with each manufacturer over technical support, reliability guarantees, performance guarantees, power by the hour rates, etc. You choose the engine that seems to give the lowest long term operational cost. The selection process can take a couple of years and right to the end it ain't over until its over.
For other equipment there are a number of approaches. Some examples:
Boeing: Equipment is either Supplier Furnished Equipment (SFE) or Buyer furnished Equipment (BFE).
With SFE you have no choice of supplier, it comes with the aircraft; an example might be the Auto Flight Control System or the Powered Flying Control Units.
For BFE, the operator can choose from a number of suppliers and negotiate the best deal they can get. Most BFE comes with a supplier's 3 year warranty. Examples might be the VHF Comms, TCAS or Navigation suite or even the galleys and lavatory modules. Cabin equipment - seats, cabinets etc. are always BFE.
Airbus: Everything is set by Airbus. You get a choice of supplier, but the price is negotiated with the supplier and fixed by Airbus. Your negotiating point with the supplier is over the support conditions - warranty terms, reliability and performance guarantees. I like to try and get agreements for free or reduced price product improvement modifications during the initial years.
The mistake many operators make is to bargain the supplier down to a rock-bottom purchase price. It looks good to the CEO and Finance people - indeed they can seldom resist interfering at this point, usually with disastrous long-term implications. The supplier will always sting you on support and without a reliability guarantee you're helpless.
The best deal for long term operating cost - the cost of ownership - is to shave a small amount from the initial price offer and drive a hard bargain on support and reliability. This is especially true for engines.