Hi Ana
1) if you plot the GCP in geographic and in SAR coordinates, the 2 pictures will not be matching, because SAR images are plotted with the range in the vertical direction and azimuth in the horizontal one. If you want to plot the SAR image in geographic coordinates, you can press the “Mean Kml” button (in the GCP selection module): you will see (in Google Earth) that everything matches. All these steps are shown in the tutorials
2) the temporary files in the Multi-Image Sparse-Points (MISP) processing module are used to spare memory and also to allow recovery of possible broken operations. However, you do not need them in normal conditions. In normal conditions, you should save your results in a permanent way through the different “save” buttons you find at the different processing steps (the most important ones are “Save Param” and “Save Coher”, but you may also want to save the read phase and APS for further use). So, if you saved your results, and if you do not want to further process the data with different options, do not worry about closing that window…
let me know this clears your doubts…
d