I haven't read that book by HE Kalu Rinpoche but the most important thing would be to practice the Four Thoughts That Turn the Mind From Samsara: precious human birth, impermanence, karma and the sufferings of samsara. Generate the mind of Bodhicitta as much as possible - the intention to gain enlightenment for the sake of all beings throughout space and time and then actualize that as you can by actually helping people when you can. They you can do Atisha's refuge prayer practice while visualizing all the Buddhas and Bodhisattvas in front of you and with you leading all sentient beings in human form in the prayer and visually imagining that yourself and all beings are doing prostrations.
As for the deity visualization, see what Kalu Rinpoche wrote in that book. People shouldn't visualize themselves in esoteric deity forms until they have had empowerment and instruction from a lama. You can visualize Chenrezig in front of you through and do the practice that way just like he was in front of you on a higher throne. Doing this will be very effective in developing and deepening love and compassion and creating auspicious interconnections.
So one way of integrating all of this is to do this in a meditation session by contemplating the Four Thoughts, then doing Atisha's efuge Prayer, then generating Bodhicitta and dedicating your meditation to save all beings from samsara and then doing the Chenresig practice and then dedicating the merit for all beings to attain perfect enlightenment. Actually I'm sure that the sadhana in the book includes these exact steps (and it has some form of refuge prayer for sure).
Atisha's Refuge Prayer is:
SANG-GYE CHO DANG SOG CHE CHO NAM LA
CHANG CHUB BAR DU DAG NEY KYAB SU CHI
DAG GEG JIN SO JIN PAY SO NAM CHI
DROL LA PEN CHER SANG-GEY DRU PAR SHOG
I don't read Tibetan but this is usually translated as
In the Buddha, Dharma and Sangha I take refuge until enlightenment is won
By the merits of giving and the other perfections
May I attain enlightenment for the sake of all beings
Giving and the other perfections refers to the six perfections of
giving, morality, patience, perseverance, meditation and wisdom (the last two are often listed as concentration and meditation).
Lam rim (at least most of Lam rim and maybe all of it) is intended to be practiced progressively and while it is better to receive it from a lama directly your circumstances don't permit that right now. But keeping reading and practicing the Lam Rim would be excellent (is this Pabonka's "Buddha in the Palm of Your Hand" ?).