Yes, xsimpleblocks is little strange theme :) but working fine on xoops 2.5.9 Most important to set some "starting" blocks configuration and also set bottom blocks as top and top blocks as bottom
For "padding/margin" problem Ill sent you PM to fix it
Hi ghia, I dont understand very well your question (my pretty eng haha), but I guess that you mean that header height is too big and hidding the content. If Im right, you can see how I did "fix" it in one of my production site with xsimplegrid theme
If you want, send me (u can PM also) your site, poin me hte problems and Ill surely help you :) Also, you sould use for 2.5.8/2.5.9 right theme, look at http://www.eunion.info/xoops/xsimplegrid/