It may depend on the type of where clause you are writing. In a simple where clause, it is generally better to have an index on the field you are using (and uindexes can and should be built on more than the PK). However, you have to write a saragble where clause for the index to make any difference. See this question for some guidelines on sarability:

What makes a SQL statement sargable?

Performance of SQL query with condition vs. without where clause
Classes can be added to an Android project in Eclipse via New -> Class, and this will supposedly add it to the project somehow, but how can I do this via the command line? I set up the class in src/(reverse.dns.path)/CLASS.java, but I couldn't find anything in http://developer.android.com/tools/building/building-cmdline.html, but I would appreciate any guidance
