The more you use it, and the longer, the hotter it will get.
My Rooted Hero would run between 88-105F, if it got any hotter I did a soft reset. But only because I was running a custom overclocked ROM.
The Stock Evo *Shouldn't* get hot enough to hurt itself. It should be programmed to turn off if it gets too got.
To see exactly how hot it is, use spare parts, and look at the battery info.
Or download "BatteryLife" it's a battery widget that will show you the current temp.
Edit: To delete the stock Bookmarks, just bring up the stock browser, hit Menu, hit bookmarks, longpress on the bookmark you would like to be deleted, a menu will pop up, click delete.
A good top for Android, when in doubt, longpress, if that doesn't work, hit menu and see what happens.