You'll have to put down a small deposit when you custom order the car. My deposit was $1K on a 2011 X6 35i.
Typically when you order the car, you also request PCD. If you search this forum and others, you'll find people who requested PCD as late as the week before the vehicle build was complete. Basically, the factory needs to catch the vehicle before it is scheduled to be transported to your dealer and have it rerouted to the Performance Center.
If you do PCD, about two weeks prior to PCD you'll have to complete the purchase transaction (downpayment + financing). If you take delivery at the dealership, you complete the purchase transaction when you take delivery there.
Pushing delivery out to 3+ months after ordering is very unusual. But, it may be possible. Check with your SA. To give you a sample timeline: I custom ordered in late October. My X6 was built by the last week of November. I completed my transaction the 1st week of December and did PCD in mid-December.
I talked to SA's at BMW of Fairfax, VOB, Russell, and Tischer. VOB got to the right price and we liked the SA. I bought there. But, I used Truecar.com to get competitive offers that VOB had to respond to.