2005 onwards(new shape) vitz 1.0 does not come in manual. The UK model Yaris comes in manual but it was very hard to find that one in Pakistan, almost all vitz here are Japanese imports.
Economy: Spark will have better economy as its engine size is smaller and its manual.
Comfort: Both are good cars. For a 800cc spark has a comfortable drive. Vitz is a slightly bigger and more expensive car so naturally its better.
Resale: Resale of vitz is far better than Spark.
Safety: Vitz is better as it comes with airbags and abs.
Part: Parts of vitz are available commonly. Parts of spark are available at authorized service centers.
Also keep in mind Vitz will be used whereas Spark will be brand new. There is also a considerable price difference between the two.