Should I resign from my job, and what if I don't find another job, knowing that the owner of the company I work for is the head of the Association of Habashis in my city and sometimes asks me to prepare donation checks for his association?

The basic principle is that it is not obligatory to quit or resign from a job unless the job itself is Haram (definition) or involves aiding in something Haram. It is not permissible to donate to associations with invalid activities, and preparing checks for them is considered aiding them. Therefore, you should strive not to do that. If it is necessary, then look for another job. There is no harm in remaining in your current job until you find an alternative.