Hollie replies:

The closer you take your birth control pill to the 'normal time' the better. That said, you do have some flexibility (you have a twelve-hour window before the pill is considered "late").

You don't sound comfortable using the birth control pill as your sole method of birth control. Have you talked to your partner about this? Many couples use condoms in addition to the birth control pill. If you both have not been tested for STIs, are monogomous, and have been so for over 6 months, you should be using condoms anyway, to prevent STIs.

Morning sickness does not appear within the first week of sex. Pregnancy doesn't even happen that fast. A missed period is most often the first sign of pregnancy, not morning sickness. The stomachache was most likely due to stress of worrying about an unplanned pregnancy. You really have no risk of pregnancy here though.

Safe, Sound & Sexy: A Safer Sex How-To
Safer Sex...for Your Heart
Sexual Negotiation for the Long Haul
STI Risk Assessment: The Cliff's Notes