Application for accommodation at the halls of residence (=dorms) of Charles University needs to be submitted in the online Erasmus registration. Some of the dormitories offer tourist accommodation, so if you arrive before the semester starts you can stay there and it will be definitely the cheapest option you´ll find in Prague.
You´ll find much more information about accommodation on the CU website. There is for example what you need to prepare for the check-in in the dorm, what are the monthly charges for the dorm, there are links for information leaflets for each of the dorms which are offered to Erasmus students (Hostivař, Větrník, Hvězda, Trója), how to apply for accommodation grant and who to inform if you decide to find an accommodation on your own. Some info about accommodation is also in the Erasmus Arrival Sheet of CU.