When I did it with the 3 Series, my salesman used the same configurator on BMW's website & once I had something I liked, it just came back to financing. After that was done & I had placed my deposit, the only headaches came from figuring out when exactly my car would come in. Took around 2 months to finally get it from the order date, but it was interesting getting updates on where exactly she was.
It can depend a lot on who you actually deal with, but it was a pretty easy process for me for the 1 time I actually had to order it. Your consultant should be able to walk you through the build process with a configurator & hopefully be knowledgeable enough to explain all the options, trims, etc. along with explaining why certain options can't be ordered together. Once you're done, they will sometimes try to find if a car meeting what you want has already been built for your convenience & can be traded to make the sale. At least, that's how my experience went; no headaches, pretty simple process beyond agreeing on the payments. I don't know how other manufacturers are, but through BMW & Lexus, it's been easy.
I would highly advise building the car yourself beforehand, & checking to see if other owners were able to order options together the manufacturer claims can not be. In the case of work for example, Lexus' website wouldn't originally allow you to order a GS350 F-Sport in Deep Sea Mica or Rivieria Red, but every couple months, one would be ordered in those colors. Or the RC-F that could be special ordered to have the Torque Vectoring diff. without the Performance Package; now packaged together. Certain things like that I imagine can make the ordering process a lot more difficult if the dealership claims they can't be done when you know owners out there have been able to; again, coming back to hopefully dealing with a salesman who actually knows his product and can help you order exactly what you want.
