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You can use quikrete to repair the holes you are going to need their resurfacing product (red bag) since your holes are very small in reality. You may well need to use a bonding agent as well, just painted onto the divot prior to applying the patch to give extra holding power.
Your main problem is going to be the acceptance of the stain, your right the original concrete will accept the stain a little different to any new concrete/patch added, there is little you can do to stop this, it won't be a great deal different and most of your holes from the tack strip should be in corners so it shouldn't be a big problem.
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