After you have a Gaijin Card and a VISA then you can get a Re-Entry permit into Japan. A Re-entry Permit will allow you to leave the country and re-enter without having to give up your Gaijin Card and without screwing up your VISA status.
You can also avoid the long lines at the airport if you have a Re-Entry permit. You’ll join the line that says “Japanese/Re-Entry Permit Only”. You’ll save a lot of time and hassle by getting this permit. Re-Entry Permits cost 3000 yen for a single one-time re-entry and 6000 yen for a multiple-use permit. Check with the Immigration Bureau of Japan for more info, updates on current immigration laws and specific locations.