From the Pathfinder SRD section defining Spell Resistance:
To affect a creature that has spell resistance, a spellcaster must make a caster level check (1d20 + caster level) at least equal to the creature's spell resistance.
So the bonus to the roll is your caster level.
Yes, they are affected by spell resistance
Even though those spell-like abilities, elemental ray and acidic ray, have no spell to base themselves on, spells (in general) and spell-like abilities are subject to spell resistance, unless otherwise noted.
Spells from the conjuration school can mostly ignore spell resistance, and spell-like abilities based on those spells follow the same rules. So a spell-like ability that duplicates Create Pit, which ignores spell resistance, would also ignore spell resistance. This can be seen on the topic When Spell Resistance Applies:
Effect Spells: Most effect spells summon or create something and are not subject to spell resistance. Sometimes, however, spell resistance applies to effect spells, usually to those that act upon a creature more or less directly, such as web.
But spell-like abilities that do not duplicate a spell (like elemental ray and acidic ray) follow a more general rule, with their spell level based on the highest spell the character can cast, as per this FAQ on SLA's:
Cleric domains, sorcerer bloodlines, wizard schools, and certain other class features give spell-like abilities that aren't based on spells. What's the effective spell level for these abilities?
The effective spell level for these spell-like abilities is equal to the highest-level spell that a character of that class could normally cast at the level the ability is gained.
For example, a 1st-level elemental bloodline sorcerer has elemental ray as a spell-like ability. Because a sorcerer 1's highest-level spell available is 1st, that spell-like ability counts as a 1st-level spell. A 9th-level elemental bloodline sorcerer has elemental blast as a spell-like ability. Because a sorcerer 9's highest-level spell available is 4th, that spell-like ability counts as a 4th-level spell.
The most reliable method of overcoming SR is to use spells that bypass it. You can use d20pfsrd.com's spells DB to filter out all spells that require a caster level check when they encounter SR, or look for "Spell Resistance: no" in the spell descriptions. Conjuration spells are especially good in this area.
As others have mentioned, buffing the party is often a good way to contribute without having to beat SR. (But note that unless they drop their SR as a standard action, allies with SR will still block applicable spells.)
Extraordinary and supernatural abilities are not affected by SR. For example, most hexes do not require caster level checks.
Finally, there was recently a thread on this subject in the Paizo forums for increasing spell penetration for those situations where SR checks are required. Cao Phen in particular provided a wonderfully comprehensive answer. Here I've copied his list, added a handful of additional niche options, and provided links to the SRD.