Hebrew and Roman scripts are very hard to mix well. Not only do you have the problem of l to r versus r to l, but also the difference in typographic 'color.' Roman has heavy verticals and light horizontals, and Hebrew is opposite.
To match typographic color somewhat, you can choose Hebrew and Roman fonts that have relatively low contrast. (See the El Al logo.) Or you can design so that you deliberately contrast the weights of the Hebrew and Roman.
Generally speaking, the easiest way to use the two together is on mirrored pages, so they don't visually clash. The traditional thing is to have the Roman on the left page and Hebrew on the right page. But some have argued, I think correctly, that the other way around is preferable as a general rule. Then you need to match the color and height of the Hebrew and Roman. Often this means that the top of the Hebrew (except the pole on the lamed) is between the x-height and cap height of the Roman—similar to a small cap of the roman.
If you keep both main and sub items with their same language, on mirrored pages, that's the easiest way. But you still have to deal with aligning mirrored passages of the same meaning, as whichever language is a translation will often be longer.
Next easiest is to have the Hebrew and Roman on separate lines. Hardest is to have Hebrew and Roman work together visually on the same line.
There is no one best way to to solve the problem of the differences in direction and color. It will depend a lot on which language you expect most of your readers to read, how you expect different readers to consult the two languages, how much text you have, your choice of fonts, and so on.
Good luck!