Yes, you must EV train Sceptile. In Gen 4, other factors associated with stat calculation (IVs, nature) cannot be manipulated, so maximising Sceptile's EVs in SpA is the best you can manage.
In Gen 4, Vitamins only have an effect for the first 100 EVs in a given stat, after which point you'll be told they have no effect. If Vitamins worked on your Sceptile and you haven't used it much since, then its current SpA EVs likely sit at 100 or slightly above. Since you can get a maximum of 255 EVs in each stat, it is possible that Sceptile could yet double its SpA EVs.
If you have been doing lots of random battles with Sceptile, then note that each Pokemon can have a maximum of 510 EVs in total. Thus, if Sceptile has accumulated more than 255 EVs in stats other than SpA (which is likely if you've battled with it a lot), then you will need to decrease its EVs in those stats using EV-reducing berries if you wish to max SpA.
When you are ready to EV train, check for ideal locations using this guide. If you have a Macho Brace or Power Lens, equip Sceptile with it. If you have Pokerus, make sure to spread it to Sceptile.
