Tools are good to take of some of the general directories and can save you time/money rather than doing those yourself. Citations won't be built as quickly however as you will need to wait at least few weeks to a month usually before they are completed. Like Colan said, if you have more than a few listings, it's probably good to go that route. Tools however won't catch all the niche specific sites and those will need to be built manually. My suggestion is to do a hybrid.
Both methods have their advantages and disadvantages. The main points of comparison are:
Speed - automatic submissions are, by default, faster than any manual method.
Time involvement - usually automatic submissions are (or at least look like) one-button-push solutions.
Cost - in most cases, automatic submissions have recurring fees attached, i.e. they are not once-and-done solutions; thus, in the long run, they are definitely more expensive, even if they might look cheaper initially.
Accuracy - automatic solutions deal, most of the times, with 1 listing per site only; they discover any existing listings automatically as well; both of these factors mean automatic submissions might do more inaccurate or incomplete job as compared to manual solutions; for instance, they might miss already existing listings and instead submit new ones + they will almost never very, very rarely deal with duplicate listings.
Flexibility - by default automatic submissions are a lot more inflexible as far as the sites they could cover are concerned; they feature pre-determined lists of sites, and these cannot be added to, removed from, or otherwise changed.
Each of these positives and negatives comes with a trade-off. For instance, while it might seem like a very seamless task to set up an account and submit listings via an automated solution, the trade-off is that neither you, nor your clients, own or have control over the listings (hence the recurring fees that apply).
In most cases, the following might be a suitable rule of thumb:
For enterprise clients (i.e. companies with more than 50 physical locations) - automatic submission to the most important citation sources, with supplementary manual audit work to discover any missed duplicate and incorrect listings + manual submissions to more sites that are not covered by the automated solution.
For very new SMBs (i.e. those who have just opened doors and have 0 online footprint) - automatic submission + manual submissions to more sites that are not covered by the automated solution (note that this does not apply to cases where a previously existing business has been acquired, merged, or re-branded).
For existing SMBs, especially ones who have made any changes to their NAP in the past (moved to a new address, changed phone numbers, re-branded, etc) - fully manual work, unless after a manual audit you discover that there is very little online footprint; in such rare cases, you can do the same as what you would with very new SMBs.
For "practice-practitioner" businesses (i.e. businesses where there might be listings for both the business and for the professionals that work at/for/with the business, typical examples are law firms, medical practices, dental practices, real estate agencies, insurance agencies, accounting firms) - fully manual work, always.
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