Subway operating hours and journey time in Guangzhou

Is it loacted at Baiyun Dadao South or near Pazhou MTR Station?
If the latter, your above-mentioned way is right. Otherwise, it should be subway line 2, then line 3.
Since you plan to check in at 07:00, it may be a little tight to take subway. They will start the operation at 06:00 or later, and the whole journey takes about an hour or more.
Therefore, you may need take taxi there for checking in, which is the most secure way.