Which way is better to put files on the internal or external storage?

I just like to get some input, to see what you guys think. Which way would be better to keep the primo files on the internal memory or the sd card. The other day I was transfering files to internal memory from PC it was going at about 1MB/s, also transfered the same files to sd card and it was going about 5MB/s, quite a difference. Is it the same for reading the data from the internal and external stoarge? Does it mean that when I run the software from internal memory would be more slower than running from SD card?
Have 7" GPS 800MHZ unit with winCE6.0 256MB RAM, 8GB internal Storage and 16GB SD card class 10.