Saved passwords are stored in cookies. And yes you will loose those if you clean out cookies. When you return to a site which asks for a password, when you re-enter it, it will be stored until you clear cookies again.
There is a (freeware) cleaner which does an effective job of cleaning up your system, and lets you selectively keep certain cookies so they are not removed. CCleaner;
http://www.majorgeeks.com/download4191.html
Once loaded and opened, survey the elements on the left which will be removed. (Default settings are good.) You can uncheck anything you don't want touched.
On the extreme left, click on Options, then click Cookies. Find the sites you trust and where you have password access on the left. Click/highlight the sites you want and then click the arrowhead in the centre to send them to the "Cookies to keep" on the right.
Then click on Advanced (still under Options). Remove the checkmark from the box for: "Only delete files in Windows Temp folders older than 48 hours"
Then click on Cleaner (top, extreme left). Click on Run Cleaner (bottom right corner).
(Some files will not be deleted until a restart is performed.)



