I live close to Woking and used to live in Woking itself. I also have commuted to London over the years for various amounts of days and hours and have been through various combinations of childcare.
If you have a choice between Woking and Guildford, I would choose Woking purely for ease of commute. I also think, whatever your budget is, you will get a bit more for your money within walking distance of Woking station rather than Guildford station. If you have to add on a car trip to the station, this will make your day even longer and car parking prices are ridiculous. Having said that, if you use a childminder you will probably end up having to drive somewhere anyway to drop them off.
Primary schools in Woking are generally good but secondary provision is not very good unless you are Catholic and can get into St John the Baptist. However, secondary is years off for you and things can change.
From every other point of view, Guildford is a better option - shopping, leisure activities, High St etc - but being realistic, work, home and school are your priorities right now and the amount of time you will have to waft around the cobble stones of Guildford from Jo Malone to Jigsaw is likely to be fairly limited!
I now work part-time and have an after-school nanny but start work late enough to be able to drop my ds2 at school beforehand. DS1 is now at secondary and so my childcare arrangements are much easier than when they were little. I use students for holiday care and have never had difficulty in recruiting one. I take most half-terms off and use grandparents for occasional inset days etc. DS1 is old enough to be home alone if necessary. If you have space, I think an aupair would be your best option. For you, a nanny will be very expensive childcare. Obviously, you can ask a good nanny to do laundry during the day, cook for children etc but seriously no nanny can be kept occupied for 6 hours a day on general household tasks and children-related activities from say, 16 April when schools went back this term to 1 June when half-term starts. Most schools will have one inset day in that period and even allowing for nanny attending say, sports day and perhaps one other school activity, and one/both children having a few days off ill that's still a lot of hours to fill for which you are paying a lot of money.
If you use an aupair and cover holidays with a combination of holiday clubs, your own holidays and possibly recruiting a student (or TA or teacher, I get applications from them) in conjunction with the aupair you still ensure a good level of care.