Kind of depends on how the recipe is formulated...
If I put the recipe into beersmith with a 5gal. boil volume for a 5gal. batch, I start with 5 gal and top-up whatever I'm left with at the end of the boil to 5gal in the fermenter. If the recipe calls for a 3 gallon boil, I start with 3 and top-up whatever I'm left with to 5 gallons, etc.
Some people like to start with a larger boil volume to end up with 5gal. at the end of the boil. I've never done this, but you would just calculate the recipe based on a 6gal. boil volume for a 5gal. batch, etc. Same as above, only you're accounting for a larger boil volume and you won't need to top-up at the end...
The reason for doing all this is to hit your target IBU's while accounting for differences in hop utilization: as boil volume increases, hop utilization increases; and vise versa.
I use hop bags during the boil for pellet hops and remove them when pouring the cooled wort into the fermenter. If using whole hops, I use a paint strainer bag stretched over the funnel to catch all the hops when pouring the cooled wort. In either scenario, there's always some trub that gets into the fermenter. This is nothing to worry about: I haven't noticed a difference between either method, even though I get more hop particles in the carboy when using pellet hops. If your beer sits on the trub for only 3 or 4 weeks, you won't notice any resulting off flavors.