You can only stack the same gem of a different rune type. So you can use a Shadow Greenstone Rune I on a Al'noth Greenstone Rune I and you will get a Shadow Al'noth Greenstone Rune I but you can't use two runes at the same time, no.
If you attempt to use say a Shadow Greenstone Rune I then a Tidal Malachite Rune I on yourself, the first one will be cancelled. If you attempt to stack them it will not be allowed.