How do I read Query Cost, and is it always a percentage?
The query cost is reported in execution plans as "estimated subtree cost". This is an absolute figure such as 1.5. Conor Cunningham mentioned in a SQLBits presentation that it originally referred to the number of seconds taken to execute on a particular Microsoft employee's machine ("Nick's Machine")  in the SQL Server 7 days 



but now should be interpreted as a unitless measure of overall cost.

The execution plan is a tree. Each iterator in the tree is given an estimated CPU cost and an estimated IO cost and these are added together to get the overall cost (the relative weightings can be adjusted with a couple of undocumented DBCC commands). The estimated subtree cost includes the cost for the iterator itself and all its descendants. To see an example of the costing formulas used you can look at this article.

To determine the estimated cost for an entire query in SSMS select the root iterator (e.g. the SELECT iterator) to the left of the graphical plan and look at this metric in the SSMS properties window.

When running multiple queries (whether in the same batch or not) the percentage is calculated by adding up all of these values and calculating the percentage as you would expect.

You should be aware that even in actual execution plans this cost figure is based on estimates and using this to compare the relative merits of two different queries can be woefully wrong in cases where the estimates are inaccurate.