staining new wood takes some prep work for a good uniform staining job.
First, the wood must be sanded down carefully from coarse to 220 grit paper. Then even passes with steel wool.
Then, the wood must be completely free of debris from sanding. I like a fox tail brush or even compressed air.
Next step should be a good quality wood conditioner spread all over the intended staining project. This really makes all the wood stain in a semi uniform manner. will eliminate splotching staining. woods stain differently within the same species because of knots, spongy material, and areas that are non pourus. Wood is a funny thing.
Then the actual staining process is obtain a good staining cloth and stain in the direction of the grain. Apply one coat, then re apply another and so on. In staining paneling, I would get a large staining sponge and make one long swath the entire length of the wood and then do another until that is completely done. Being careful not to do too much overlaping and un loading too much stain in one point. When dry, then re apply and make sure that all panels are stained the same and with the same amount of coats.
Feathering out is very important so that you get a uniform stain job.