Recommendations for a car stereo set-up?

Most likely your HU will have more watts then that 45w amp you were considering. I would bet your 6x9s are rated at well over 100w. I cant stress this enough your quality is only as good as the wiring and install dont cheap out there. Depending on the OHM rating of your 6x9s get a amp that will be compatiable with the OHM rating of the 6x9s. If considering a sub later you may want to run the amp to the sub and your inside speakers to your HU.