There's two main things to get used to about the App Engine datastore when compared to 'traditional' relational databases:
- The datastore makes no distinction between inserts and updates. When you call put() on an entity, that entity gets stored to the datastore with its unique key, and anything that has that key gets overwritten. Basically, each entity kind in the datastore acts like an enormous map or sorted list.
- Querying, as you alluded to, is much more limited. No joins, for a start.
The key thing to realise - and the reason behind both these differences - is that Bigtable basically acts like an enormous ordered dictionary. Thus, a put operation just sets the value for a given key - regardless of any previous value for that key, and fetch operations are limited to fetching single keys or contiguous ranges of keys. More sophisticated queries are made possible with indexes, which are basically just tables of their own, allowing you to implement more complex queries as scans on contiguous ranges.
Once you've absorbed that, you have the basic knowledge needed to understand the capabilities and limitations of the datastore. Restrictions that may have seemed arbitrary probably make more sense.
The key thing here is that although these are restrictions over what you can do in a relational database, these same restrictions are what make it practical to scale up to the sort of magnitude that Bigtable is designed to handle. You simply can't execute the sort of query that looks good on paper but is atrociously slow in an SQL database.
In terms of how to change how you represent data, the most important thing is precalculation. Instead of doing joins at query time, precalculate data and store it in the datastore wherever possible. If you want to pick a random record, generate a random number and store it with each record. There's a whole cookbook of these sort of tips and tricks here