Hi @Centauri,
You are correct that the Spark Core runs at 3.3V. However there are a number of ways to work with a 5V circuit.
The Shield Shield will convert between 3.3V and 5V, so you should be able to use any 5V Arduino shield with the Spark Core.
Most of the pins are 5V tolerant, with the exception of the analog pins (A0 to A7) and D2 which are only 3.3V tolerant. This information is documented on the Spark Core github page, and will be further documented (more clearly) when our new documentation page is published.
The Spark Core is also intended to run off of 5V power, which it regulates down to 3.3V. This is how it is powered off of USB, which is 5V. If you connect your 5V power source to the RAW pin, it will be regulated down to 3.3V, and the VCC pin will be a 3.3V output.
Hope that helps!
Zach
EDIT: I forgot about D2 when I first wrote this post, so edited this post to be correct.