Processors will use the Work number, if not available they will physically call a number given to them (HR, manager) that can confirm employment- nothing more nothing less. Having 2 jobs doesn't matter, it's not like they contact HR and say that you have another job elsewhere. You're all good for the employment and yes you can use both W2's to income qualify.
You have had both jobs for over 2 years so there should be no issue. They will add the incomes together and get the total amount for the year and then divide by 12 for your monthly income and then do the debt to income ratios from that number.
On verification, they could verify over the phone, by fax, or by email, or through a service that gets your information from your HR or payroll department (Paychex, ADP or a service like "The Work Number"). It all depends on what your employer set up to verify and how the processor/underwriter verifies. Every company is different and it does not matter the size of the company, its is a choice every company makes.
I don't do any verifications of our employees over the phone. I make the lender fax or email me, including the copy of the release from the emplyee, and then I verify with the employee (in private) that they were expecting an employment verification. This is just in case it is a scam.
If they do send the wrong verification to the wrong employer, just play it off as they sent the one that was suppose to go to ...(your spouse, or girlfriend/boyfriend, brother/sister) and let it go, don't make a big deal about it. This occasionally happens even though it is not suppose to. Call the lender and tell them what happen and have them resend the correct request.
Another way they will double check is by having you sign an IRS 4506 form for your past 2-4 years tax returns at the IRS. This is where they find a lot of discrepencies. If what you put down on wages (W2) doesn't match what was reported to the IRS they are going to want to know why.
