Good finish depends on good prep, and that you can't rush. Looks like you're working with two different kinds of wood between the frame and the plywood, and they will take the stain differently. With pine you can have problems from sappy knots and with sap wood when sanding and staining with the long grain. Pine is a soft wood but within it there are areas that are much harder and softer than others and these areas will take stain differently.
The "primer" referred to on the can is actually a stain controller, for pine, that limits the differences between the soft and hard areas keeping it from getting blotches. This also causes the whole staining job to appear a bit lighter so try it on the bottom first.
Don't go any finer than the 120 grit on your prep sand 'cuz with pine a finer grit will tend to clog the grain and again restrict the stain uptake by the wood. Always sand and apply your finishes with the grain and between any sanding, whether you paint or stain, use tack cloth to pick up the fine dust that you can't wipe or vacuum off.
In this day and age of low VOC finishes, especially in California where I don't think you can even buy alkyd /oil any more, you'll probably be workin' with water based products. Be mindful that your plywood finish ply (which I couldn't I.D. from the pics) can be sanded thru very easily, and... if it is a luan type, the surface ply may be a tropical mahogany like wood whose grain will tend to raise and get fuzzy from the water in the stain. Again...try it all on a hidden part first so you don't run into any unexpected surprises. Consider it an homage to Mr. Murphy and the wood gods, who are lookin' to get even with every wood worker for cuttin' down trees.
For future reference, you can't beat epoxy paints for toughness, chemicals and moisture resistance. I haven't used this one but it's similar to a local product that I have used on boat refurbs. Epoxy is what people use to paint garage floors and swimming pools, takes a lickin'.
http://www.aquaticeco.com/subcategories/3048/Epoxy-Paint-1-Gallon
If possible try staining a piece on the bottom edge first to check your final color and finish when dry. The stain depends a lot on how you apply it so consistency is key.
As far as practicality of finish, it sounds as though you may be a student? If so and this set up is going to see a few moves in its life, return the stain and buy the paint. Much faster, much more durable and easier to repair.
Wear a respirator when sanding and painting. Gloves and eye protection as well. Just like fish, we can soak bad stuff up thru our skin, eyes, mouth and belly button, (fish don't have belly buttons do they?) The reason I've got time to spend on aquariums is because I worked in a cabinet shop where we didn't.
Good luck!