It should be fine, it's better if you have some sort of filling device e.g. counterfiller or beergun but you'll get away with more low tech methods if it's for near instant drinking. Make sure the bottles are very cold as this will help to reduce foaming, you will most likely lose some carbonation but that's hard to avoid without the gadgets.
edit: I haven't tried this but apparently it's easy to make your own filler[/url:2a5cihq0]