Glasgow has a lot of well stocked whisky bars but Edinburgh is probably best for whisky shops.
If you visit Edinburgh, you could visit the Heritage Centre, (by the Castle on the Royal Mile), but perhaps only for the bar there, the tour is OK but if you have visited distilleries and have a bit of knowledge it might be a waste of your money.
On the Royal Mile most bars carry a genourous range of malts, with the Albanach, (0n the corner of Cockburn st) having a particularly good range and The Malt Shovel down on Cockburn st are good on their prices. For Shops, Oddbins, Royal Mile Whiskies and down on the Cannongate there is Cadenhead, (all on the Royal Mile). You have to visit the Bow Bar on Victoria st, (just off the Royal Mile on the right hand side coming down from the castle), for real ales and a fine whisky selection. The Whisky Shop is directly across the road from the Bow Bar, (Whisky Shop in Princes Mall is currently closed for refurbishment).
Away from the old town area you have the Canny Man, (morningside), Bennets, (Tollcross), Mathers, (west End) which are all good bars.
Plenty to enjoy for one day!!
In Glasgow, I am not sure if Robert Graham has re-opened since it caught fire last year. And I would second the trip to either Glengoyne or Auchentoshan.